Origin IGS: agaaaaaacgtttcacattcctttaaatttcttgtaaatcatctcaagttcatcctgaaagaaagaggccttatcaagataaaatagataaaaatgctacctatattataccccatttagaggagattaggtagcaagtttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caaacttgctacctaatctcctctaaatggggtataatataggtagcatttttatctattttatcttgataaggcctctttctttcaggatgaacttgagatgatttacaagaaatttaaaggaatgtgaaacgttttttct Mask Tandem Repeat Region ================================================ agaaaaaacgtttcacattcctttaaatttcttgtaaatcatctcaagttcatcctgaaagaaagaggccttatcaagataaaatagataaaaatgctacctatattataccccatttagaggagattaggtagcaagtttg Find is-nt database================================================ Query_seq: SMT_1519:SMT_1520|SMT_1519:SMT_1520:DNA-binding response regulator VncR:K02004:<-<-:1499753..1499894 142 agaaaaaacgtttcacattcctttaaatttcttgtaaatcatctcaagttcatcctgaaagaaagaggccttatcaagataaaatagataaaaatgctacctatattataccccatttagaggagattaggtagcaagtttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1519:SMT_1520|SMT_1519:SMT_1520:DNA-binding response regulator VncR:K02004:<-<-:1499753..1499894 142 agaaaaaacgtttcacattcctttaaatttcttgtaaatcatctcaagttcatcctgaaagaaagaggccttatcaagataaaatagataaaaatgctacctatattataccccatttagaggagattaggtagcaagtttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1519:SMT_1520|SMT_1519:SMT_1520:DNA-binding response regulator VncR:K02004:<-<-:1499753..1499894 142 agaaaaaacgtttcacattcctttaaatttcttgtaaatcatctcaagttcatcctgaaagaaagaggccttatcaagataaaatagataaaaatgctacctatattataccccatttagaggagattaggtagcaagtttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaaaaacgtttcacattcctttaaatttcttgtaaatcatctcaagttcatcctgaaagaaagaggccttatcaagataaaatagataaaaatgctacctatattataccccatttagaggagattaggtagcaagtttg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 27 End: 131 .......................... M S C K S S Q V H P E R K R P Y Q D K I D K N A T Y I I P H L E E I R ........... agaaaaaacgtttcacattcctttaaatttcttgtaaatcatctcaagttcatcctgaaagaaagaggccttatcaagataaaatagataaaaatgctacctatattataccccatttagaggagattaggtagcaagtttg 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================================================ agaaaaaacgtttcacattcctttaaatttcttgtaaatcatctcaagttcatcctgaaagaaagaggccttatcaagataaaatagataaaaatgctacctatattataccccatttagaggagattaggtagcaagtttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1519:SMT_1520|SMT_1519:SMT_1520:DNA-binding response regulator VncR:K02004:<-<-:1499753..1499894 142 agaaaaaacgtttcacattcctttaaatttcttgtaaatcatctcaagttcatcctgaaagaaagaggccttatcaagataaaatagataaaaatgctacctatattataccccatttagaggagattaggtagcaagtttg Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: smit_SMT_1519_SMT_1520|DNA-binding response regulator VncR:K02004|NEGATIVE:NEGATIVE|[1499753,1499894]|142 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 agaaaaaacgtttcacattcctttaaatttcttgtaaatcatctcaagttcatcctgaaagaaagaggccttatcaagataaaatagataaaaatgctacctatattataccccatttagaggagattaggtagcaagtttg agaaaaaacgtttcacattcctttaaatttcttgtaaatcatctcaagttcatcctgaaagaaagaggccttatcaagataaaatagataaaaatgctacctatattataccccatttagaggagattaggtagcaagtttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAAAACGUUUCACAUUCCUUUAAAUUUCUUGUAAAUCAUCUCAAGUUCAUCCUGAAAGAAAGAGGCCUUAUCAAGAUAAAAUAGAUAAAAAUGCUACCUAUAUUAUACCCCAUUUAGAGGAGAUUAGGUAGCAAGUUUG .....((((....................((((((((....(((....(((.....)))....)))....))).)))))...............(((((((((.(((...((.(.....).)).)))))))))))).)))). (-22.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAACUUGCUACCUAAUCUCCUCUAAAUGGGGUAUAAUAUAGGUAGCAUUUUUAUCUAUUUUAUCUUGAUAAGGCCUCUUUCUUUCAGGAUGAACUUGAGAUGAUUUACAAGAAAUUUAAAGGAAUGUGAAACGUUUUUUCU ......(((((((((....((((.....)))).......)))))))))...((((((..((((((((((.((((......))))))))))))))....))))))...............((((((((.....)))))))).. (-35.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 832 80 31 171 122 smit:SMT_1519|5end_DNA-binding_response_regulator_VncR_1499662..1499892_NEGATIVE 310 90 42 138 79 smit:SMT_885|5end_single-stranded-DNA-specific_exonuclease_RecJ_832660..832890_NEGATIVE 287 77 39 96 58 smit:SMT_1670|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1658613..1658843_POSITIVE 242 135 96 222 186 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 242 135 96 222 186 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 234 138 94 145 92 smit:SMT_937|5end_dipeptidase_889579..889809_POSITIVE 234 138 94 145 92 smit:SMT_932|5end_tellurite_resistance_protein_885065..885295_POSITIVE 234 131 94 181 147 smit:SMT_213|5end_leucyl-tRNA_synthetase_145392..145622_POSITIVE 232 50 2 207 157 smit:SMT_365|5end_hypothetical_protein_301485..301715_POSITIVE 230 139 99 56 14 smit:SMT_445|5end_hypothetical_protein_384309..384539_POSITIVE 224 135 96 71 20 smit:SMT_356|5end_hypothetical_protein_292394..292624_POSITIVE 223 140 111 212 174 smit:SMT_1063|5end_preprotein_translocase_SecA_subunit_1000714..1000944_POSITIVE 220 60 11 109 54 smit:SMT_649|5end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase_557351..557581_NEGATIVE 220 70 21 133 94 smit:SMT_136|5end_hypothetical_protein_predicted_by_Glimmer/Critica_87314..87544_POSITIVE 219 89 55 213 177 smit:SMT_1341|5end_putative_cell_division_protein_1319115..1319345_NEGATIVE 215 138 95 49 5 smit:SMT_1107|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1048081..1048311_NEGATIVE 215 138 95 158 114 smit:SMT_1106|5end_ribonuclease_P_protein_component_1047972..1048202_NEGATIVE 214 69 22 165 109 smit:SMT_1348|5end_exoribonuclease_II_1327502..1327732_NEGATIVE 214 70 37 57 23 smit:SMT_745|5end_glycosyl_transferase,_group_1_family_protein_650387..650617_NEGATIVE 213 136 99 157 112 smit:SMT_1865|5end_D-alanyl_carrier_protein_1827058..1827288_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 139 99 130 87 smit:SMT_1637|3end_hypothetical_protein_1623848..1623998_POSITIVE 255 79 55 61 35 smit:SMT_1814|3end_amino_acid_transporter_1788640..1788790_POSITIVE 244 134 94 70 18 smit:SMT_1177|3end_immunoglobulin_A1_protease_1129193..1129343_NEGATIVE 233 132 94 61 17 smit:SMT_1741|3end_surface_protein_PspA_precursor_1722303..1722453_NEGATIVE 223 140 111 66 28 smit:SMT_1062|3end_hypothetical_protein_1000648..1000798_POSITIVE 221 57 16 106 66 smit:SMT_120|3end_hypothetical_protein_72943..73093_POSITIVE 219 89 55 52 16 smit:SMT_1342|3end_protease_maturation_protein,_putative_1319276..1319426_NEGATIVE 215 138 95 141 97 smit:SMT_1107|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1047989..1048139_NEGATIVE 214 69 22 63 7 smit:SMT_1349|3end_K03075_preprotein_translocase_SecG_subunit_1327604..1327754_NEGATIVE 214 70 37 67 33 smit:SMT_746|3end_LPS_biosynthesis_protein_650377..650527_NEGATIVE 214 80 38 144 103 smit:SMT_128|3end_K03449_MFS_transporter,_CP_family,_cyanate_transporter_78702..78852_NEGATIVE 209 99 52 62 3 smit:SMT_1529|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1512776..1512926_NEGATIVE 209 125 93 116 80 smit:SMT_1392|3end_dihydroxyacetone_kinase_1369186..1369336_POSITIVE 208 140 95 105 56 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 207 56 18 42 4 smit:SMT_350|3end_immunity_protein_BlpL_290348..290498_POSITIVE 206 68 21 82 36 smit:SMT_594|3end_lysyl-tRNA_synthetase_510348..510498_NEGATIVE 203 80 36 69 30 smit:SMT_2165|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2039630..2039780_POSITIVE 202 73 31 142 97 smit:SMT_2026|3end_K03466_DNA_segregation_ATPase_FtsK/SpoIIIE,_S-DNA-T_family_1941905..1942055_NEGATIVE 197 80 31 42 3 smit:SMT_637|3end_lactose_phosphotransferase_system_repressor_543105..543255_POSITIVE 193 71 47 64 39 smit:SMT_462|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_400414..400564_NEGATIVE