Origin IGS: cgatttctaacagttgcaactccttttttgagactaagtagataatattattcttaaaactctcctagagcaaaatagctactaggagagttttttctctaatcagaagatacgtgacgggactaaaaacaatctcatctgctttgcggatgagggttttcttattttgtgctatacttaagat .........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 atcttaagtatagcacaaaataagaaaaccctcatccgcaaagcagatgagattgtttttagtcccgtcacgtatcttctgattagagaaaaaactctcctagtagctattttgctctaggagagttttaagaataatattatctacttagtctcaaaaaaggagttgcaactgttagaaatcg Mask Tandem Repeat Region ================================================ cgatttctaacagttgcaactccttttttgagactaagtagataatattattcttaaaactctcctagagcaaaatagctactaggagagttttttctctaatcagaagatacgtgacgggactaaaaacaatctcatctgctttgcggatgagggttttcttattttgtgctatacttaagat Find is-nt database================================================ Query_seq: SMT_406:SMT_407|SMT_406:SMT_407:hypothetical protein:para-aminobenzoate synthetase component I / 4-amino-4-deoxychorismate lyase:->->:351321..351504 184 cgatttctaacagttgcaactccttttttgagactaagtagataatattattcttaaaactctcctagagcaaaatagctactaggagagttttttctctaatcagaagatacgtgacgggactaaaaacaatctcatctgctttgcggatgagggttttcttattttgtgctatacttaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_406:SMT_407|SMT_406:SMT_407:hypothetical protein:para-aminobenzoate synthetase component I / 4-amino-4-deoxychorismate lyase:->->:351321..351504 184 cgatttctaacagttgcaactccttttttgagactaagtagataatattattcttaaaactctcctagagcaaaatagctactaggagagttttttctctaatcagaagatacgtgacgggactaaaaacaatctcatctgctttgcggatgagggttttcttattttgtgctatacttaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_406:SMT_407|SMT_406:SMT_407:hypothetical protein:para-aminobenzoate synthetase component I / 4-amino-4-deoxychorismate lyase:->->:351321..351504 184 cgatttctaacagttgcaactccttttttgagactaagtagataatattattcttaaaactctcctagagcaaaatagctactaggagagttttttctctaatcagaagatacgtgacgggactaaaaacaatctcatctgctttgcggatgagggttttcttattttgtgctatacttaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgatttctaacagttgcaactccttttttgagactaagtagataatattattcttaaaactctcctagagcaaaatagctactaggagagttttttctctaatcagaagatacgtgacgggactaaaaacaatctcatctgctttgcggatgagggttttcttattttgtgctatacttaagat Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 75 End: 182 .......................................................................... M A T R R V F S L I R R Y V T G L K T I S S A L R M R V F L F C A I L K .. Protein_Len: 39 Strand: - Start: 68 End: 184 ................................................................... L L I A V L L T K E R I L L Y T V P S F V I E D A K R I L T K K N Q A I S L M cgatttctaacagttgcaactccttttttgagactaagtagataatattattcttaaaactctcctagagcaaaatagctactaggagagttttttctctaatcagaagatacgtgacgggactaaaaacaatctcatctgctttgcggatgagggttttcttattttgtgctatacttaagat 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================================================ cgatttctaacagttgcaactccttttttgagactaagtagataatattattcttaaaactctcctagagcaaaatagctactaggagagttttttctctaatcagaagatacgtgacgggactaaaaacaatctcatctgctttgcggatgagggttttcttattttgtgctatacttaagat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.6 Tail_Score: -5.39721 Start: 60 End: 90 Full_Region: ATATTATTCTTAAAA CTCTCCTAGAGC AAAATA GCTACTAGGAGAG TTTTTTCTCTAATCA ...........................................................CTCTCCTAGAGCAAAATAGCTACTAGGAGAG.............................................................................................. TransTerm Strand: - Conf: 89 HP_score: -10.6 Tail_Score: -4.12456 Start: 60 End: 90 Full_Region: tgattagagaaaaaa ctctcctagtagc tatttt gctctaggagag ttttaagaataatat ...........................................................ctctcctagtagctattttgctctaggagag.............................................................................................. TransTerm Strand: + Conf: 90 HP_score: -7.1 Tail_Score: -5.12916 Start: 132 End: 156 Full_Region: ACGGGACTAAAAACA ATCTCATCTGC TTT GCGGATGAGGG TTTTCTTATTTTGTG ...................................................................................................................................ATCTCATCTGCTTTGCGGATGAGGG............................ TransTerm Strand: + Conf: 86 HP_score: -10.6 Tail_Score: -3.65309 Start: 133 End: 155 Full_Region: CGGGACTAAAAACAA TCTCATCTGC TTT GCGGATGAGG GTTTTCTTATTTTGT ....................................................................................................................................TCTCATCTGCTTTGCGGATGAGG............................. TransTerm Strand: + Conf: 84 HP_score: -11.9 Tail_Score: -2.76745 Start: 134 End: 154 Full_Region: GGGACTAAAAACAAT CTCATCTGC TTT GCGGATGAG GGTTTTCTTATTTTG .....................................................................................................................................CTCATCTGCTTTGCGGATGAG.............................. Find igs database================================================ Query_seq: SMT_406:SMT_407|SMT_406:SMT_407:hypothetical protein:para-aminobenzoate synthetase component I / 4-amino-4-deoxychorismate lyase:->->:351321..351504 184 cgatttctaacagttgcaactccttttttgagactaagtagataatattattcttaaaactctcctagagcaaaatagctactaggagagttttttctctaatcagaagatacgtgacgggactaaaaacaatctcatctgctttgcggatgagggttttcttattttgtgctatacttaagat Intra-Species Hit: Count: 1 Min: 1 Max: 184 Len: 184 Subject: smit_SMT_406_SMT_407|hypothetical protein:para-aminobenzoate synthetase component I / 4-amino-4-deoxychorismate lyase|POSITIVE:POSITIVE|[351321,351504]|184 HSP 1 e-value: 1.0E-100 bit: 365.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 cgatttctaacagttgcaactccttttttgagactaagtagataatattattcttaaaactctcctagagcaaaatagctactaggagagttttttctctaatcagaagatacgtgacgggactaaaaacaatctcatctgctttgcggatgagggttttcttattttgtgctatacttaagat cgatttctaacagttgcaactccttttttgagactaagtagataatattattcttaaaactctcctagagcaaaatagctactaggagagttttttctctaatcagaagatacgtgacgggactaaaaacaatctcatctgctttgcggatgagggttttcttattttgtgctatacttaagat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAUUUCUAACAGUUGCAACUCCUUUUUUGAGACUAAGUAGAUAAUAUUAUUCUUAAAACUCUCCUAGAGCAAAAUAGCUACUAGGAGAGUUUUUUCUCUAAUCAGAAGAUACGUGACGGGACUAAAAACAAUCUCAUCUGCUUUGCGGAUGAGGGUUUUCUUAUUUUGUGCUAUACUUAAGAU .((((((((..(((..(((........)))..)))...)))).............((((((((((((((((......))).)))))))))))))......))))...((.((((.((..(((....((((...(((((((((...))))))))).)))))))..)).))))))........... (-49.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUAAGUAUAGCACAAAAUAAGAAAACCCUCAUCCGCAAAGCAGAUGAGAUUGUUUUUAGUCCCGUCACGUAUCUUCUGAUUAGAGAAAAAACUCUCCUAGUAGCUAUUUUGCUCUAGGAGAGUUUUAAGAAUAAUAUUAUCUACUUAGUCUCAAAAAAGGAGUUGCAACUGUUAGAAAUCG .(((..(((..............((((((.((((((.((...)).))))))...))))))...........(((.(((((..((.((((.(((((((((((((.(((......)))))))))))))))).(((.........)))......)))).))..))))).))).)))...)))..... (-49.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 180 132 90 41 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 294 153 113 66 17 smit:SMT_513|5end_16S_rRNA_processing_protein_RimM_440869..441099_POSITIVE 289 159 113 126 69 smit:SMT_320|5end_alcohol_dehydrogenase,_zinc-containing_259492..259722_NEGATIVE 285 156 116 58 15 smit:SMT_2117|5end_transcription-repair_coupling_factor_2004560..2004790_NEGATIVE 276 159 120 177 136 smit:SMT_1328|5end_hypothetical_protein_1304468..1304698_NEGATIVE 264 123 82 220 174 smit:SMT_1827|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1797568..1797798_POSITIVE 264 123 82 60 14 smit:SMT_1826|5end_ATP_synthase_beta_chain_1797408..1797638_POSITIVE 264 123 82 60 14 smit:SMT_586|5end_ATP_synthase_F1,_beta_subunit_502533..502763_POSITIVE 263 180 145 120 79 smit:SMT_1572|5end_excinuclease_ABC_subunit_B_1564402..1564632_POSITIVE 262 170 139 35 1 smit:SMT_930|5end_ATP-dependent_RNA_helicase_884435..884665_NEGATIVE 262 80 32 127 74 smit:SMT_595|5end_phosphoglycerate_mutase_512593..512823_NEGATIVE 259 120 77 66 16 smit:SMT_919|5end_hypothetical_protein_872499..872729_NEGATIVE 257 178 139 98 58 smit:SMT_1890|5end_hypothetical_protein_1843407..1843637_POSITIVE 256 180 135 186 132 smit:SMT_832|5end_hypothetical_protein_775104..775334_NEGATIVE 254 149 105 66 23 smit:SMT_204|5end_K02012_iron(III)_transport_system_substrate-binding_protein_135971..136201_NEGATIVE 252 166 129 150 118 smit:SMT_1752|5end_N-(5'-phosphoribosyl)-anthranilate_isomerase_1729772..1730002_POSITIVE 250 163 121 197 142 smit:SMT_868|5end_D-alanyl-D-alanine_carboxypeptidase_817225..817455_NEGATIVE 246 174 136 231 181 smit:SMT_1342|5end_protease_maturation_protein,_putative_1320214..1320444_NEGATIVE 245 156 113 225 187 smit:SMT_1217|5end_hypothetical_protein_1176603..1176833_NEGATIVE 242 162 121 222 180 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 94 60 35 1 smit:SMT_406|3end_hypothetical_protein_351260..351410_POSITIVE 301 180 132 71 22 smit:SMT_1611|3end_K05896_segregation_and_condensation_protein_A_1600113..1600263_POSITIVE 293 157 118 66 26 smit:SMT_1553|3end_K04074_cell_division_initiation_protein_1536868..1537018_POSITIVE 273 120 81 133 90 smit:SMT_1580|3end_MutT/NUDIX_family_protein_1573153..1573303_POSITIVE 270 154 112 52 5 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 270 175 131 94 58 smit:SMT_1535|3end_exodeoxyribonuclease_V_alpha_chain_1520513..1520663_POSITIVE 268 130 81 142 90 smit:SMT_1573|3end_MutT/NUDIX_family_protein_1566960..1567110_POSITIVE 263 180 145 43 2 smit:SMT_1571|3end_CAAX_amino_terminal_protease_family_protein_1564405..1564555_POSITIVE 262 80 32 130 77 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE 257 178 139 78 38 smit:SMT_1889|3end_hypothetical_protein_1843467..1843617_POSITIVE 256 180 135 107 53 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 245 156 113 140 102 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 242 152 113 65 24 smit:SMT_1979|3end_possible_cell_surface_protein_1910282..1910432_NEGATIVE 239 164 132 43 5 smit:SMT_512|3end_hypothetical_protein_440918..441068_POSITIVE 237 110 61 108 56 smit:SMT_1767|3end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_1743243..1743393_NEGATIVE 235 60 18 137 95 smit:SMT_345|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_284803..284953_POSITIVE 232 108 61 136 71 smit:SMT_1885|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1839830..1839980_NEGATIVE 230 149 112 59 20 smit:SMT_1682|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_1666373..1666523_POSITIVE 230 86 60 113 86 smit:SMT_339|3end_K03687_molecular_chaperone_GrpE_278490..278640_POSITIVE 225 178 131 149 109 smit:SMT_1625|3end_DNA_polymerase_IV_1615066..1615216_POSITIVE