Origin IGS: gcagaaactctctatctttttttggtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaaactataaggaggacgcag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctgcgtcctccttatagttttaaaaagttgcgcctctttttaacaacattatatcatatatctaacttaatgcaatttataaatgtcattttgtaaaattttattaacaaaaaactctctaccaaaaaaagatagagagtttctgc Mask Tandem Repeat Region ================================================ gcagaaactctctatctttttttggtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaaactataaggaggacgcag Find is-nt database================================================ Query_seq: SMT_393:SMT_394|SMT_393:SMT_394:hypothetical protein predicted by Glimmer/Critica:K07729 putative transcriptional regulator:->->:324254..324399 146 gcagaaactctctatctttttttggtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaaactataaggaggacgcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_393:SMT_394|SMT_393:SMT_394:hypothetical protein predicted by Glimmer/Critica:K07729 putative transcriptional regulator:->->:324254..324399 146 gcagaaactctctatctttttttggtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaaactataaggaggacgcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_393:SMT_394|SMT_393:SMT_394:hypothetical protein predicted by Glimmer/Critica:K07729 putative transcriptional regulator:->->:324254..324399 146 gcagaaactctctatctttttttggtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaaactataaggaggacgcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcagaaactctctatctttttttggtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaaactataaggaggacgcag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 54 End: 146 ..................................................... L I V N I F Q M L N S I H Y L T T L F L R L K K F S Y P P R M gcagaaactctctatctttttttggtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaaactataaggaggacgcag 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================================================ gcagaaactctctatctttttttggtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaaactataaggaggacgcag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_393:SMT_394|SMT_393:SMT_394:hypothetical protein predicted by Glimmer/Critica:K07729 putative transcriptional regulator:->->:324254..324399 146 gcagaaactctctatctttttttggtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaaactataaggaggacgcag Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: smit_SMT_393_SMT_394|hypothetical protein predicted by Glimmer/Critica:K07729 putative transcriptional regulator|POSITIVE:POSITIVE|[324254,324399]|146 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 gcagaaactctctatcnnnnnnnggtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaaactataaggaggacgcag gcagaaactctctatctttttttggtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaaactataaggaggacgcag Inter-species Hit: Count: 3 Min: 25 Max: 129 Len: 105 Subject: NC_008533_SPD_1255_SPD_1256|ABC transporter, ATP-binding protein:peptidase, U32 family protein|NEGATIVE:NEGATIVE|[1283878,1284381]|504 HSP 1 e-value: 4.0E-50 bit: 198.0 Len: 104 Query Start:25 Query End:128 Subject Strand: NEGATIVE Subject Start: 174 Subject End: 277 ........................gtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaa.................. ........................gtagagagttttttgttaataaaattttacaaaatgacatttatatattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaa.................. Subject: NC_003098_spr1281_spr1282|ABC transporter ATP-binding protein - multidrug efflux:hypothetical protein|NEGATIVE:NEGATIVE|[1276347,1276850]|504 HSP 1 e-value: 4.0E-50 bit: 198.0 Len: 104 Query Start:25 Query End:128 Subject Strand: NEGATIVE Subject Start: 174 Subject End: 277 ........................gtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaa.................. ........................gtagagagttttttgttaataaaattttacaaaatgacatttatatattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaa.................. Subject: NC_003028_SP_1426_SP_1427|ABC transporter, ATP-binding protein:peptidase, U32 family|NEGATIVE:NEGATIVE|[1345653,1345986]|334 HSP 1 e-value: 5.0E-46 bit: 184.0 Len: 105 Query Start:25 Query End:129 Subject Strand: NEGATIVE Subject Start: 4 Subject End: 108 ........................gtagagagttttttgttaataaaattttacaaaatgacatttataaattgcattaagttagatatatgatataatgttgttaaaaagaggcgcaactttttaaaa................. ........................gtagagagttttttgttaataaaatttcacaaaatgacatttatatattgcattaagttagatatatgatataatattgttaaaaagaggcgcaactttttaaaa................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAGAGAGUUUUUUGUUAAUAAAAUUUUACAAAAUGACAUUUAUAAAUUGCAUUAAGUUAGAUAUAUGAUAUAAUGUUGUUAAAAAGAGGCGCAACUUUUUAAAA (((((..(((((((((.((......)).)))))).))).))))).(((.((((((.((((......)))).)))))).)))..((((((......)))))).... (-14.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAAAAAGUUGCGCCUCUUUUUAACAACAUUAUAUCAUAUAUCUAACUUAAUGCAAUUUAUAAAUGUCAUUUUGUAAAAUUUUAUUAACAAAAAACUCUCUAC ..((((((((........)))))))).......................((((((.((((((((((......))))).))))).))))))............... ( -8.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 194 94 56 223 182 smit:SMT_399|5end_cytochrome_c-type_biogenesis_protein_CcdA_328366..328596_POSITIVE 191 67 24 177 127 smit:SMT_151|5end_K02073_D-methionine_transport_system_substrate-binding_protein_99474..99704_POSITIVE 173 90 67 47 24 smit:SMT_593|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_509398..509628_POSITIVE 172 100 76 210 177 smit:SMT_1695|5end_ribulose-phosphate_3-epimerase_1677563..1677793_POSITIVE 161 100 75 141 110 smit:SMT_341|5end_ThiJ/PfpI_family_protein_280969..281199_POSITIVE 160 94 52 90 45 smit:SMT_622|5end_methionine_aminopeptidase_528939..529169_POSITIVE 156 93 55 52 10 smit:SMT_793|5end_K02029_polar_amino_acid_transport_system_permease_protein_703236..703466_NEGATIVE 152 100 53 181 138 smit:SMT_487|5end_transcriptional_regulator,_TetR_family_422380..422610_POSITIVE 148 43 4 72 29 smit:SMT_919|5end_hypothetical_protein_872499..872729_NEGATIVE 143 100 76 207 174 smit:SMT_817|5end_aminotransferase_728699..728929_NEGATIVE 142 96 68 230 201 smit:SMT_392|5end_acetyltransferase,_GNAT_family_323616..323846_POSITIVE 141 90 76 230 216 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 141 97 60 65 31 smit:SMT_911|5end_hypothetical_protein_862023..862253_POSITIVE 141 93 56 137 113 smit:SMT_467|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_404329..404559_POSITIVE 139 89 47 146 110 smit:SMT_813|5end_acetyltransferase,_GNAT_family_722322..722552_NEGATIVE 138 91 61 207 178 smit:SMT_1588|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1577062..1577292_POSITIVE 135 91 55 211 166 smit:SMT_1871|5end_modification_methylase,_HemK_family_1830501..1830731_NEGATIVE 134 93 55 214 172 smit:SMT_1374|5end_uridylate_kinase_1353020..1353250_NEGATIVE 134 31 1 165 139 smit:SMT_971|5end_hypothetical_protein_918965..919195_NEGATIVE 133 99 55 64 20 smit:SMT_640|5end_PTS_system,_lactose-specific_IIBC_component_546790..547020_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 208 99 56 66 15 smit:SMT_398|3end_hypothetical_protein_328279..328429_POSITIVE 187 39 3 44 5 smit:SMT_1016|3end_alcohol_dehydrogenase,_zinc-containing_953057..953207_NEGATIVE 173 90 67 37 14 smit:SMT_592|3end_amino_acid_ABC_transporter,_ATP-binding_protein_509468..509618_POSITIVE 166 99 53 62 21 smit:SMT_2074|3end_dTDP-glucose_4,6-dehydratase_1977802..1977952_POSITIVE 160 94 52 130 85 smit:SMT_621|3end_K03346_replication_initiation_and_membrane_attachment_protein_529059..529209_POSITIVE 159 100 51 80 26 smit:SMT_1470|3end_K06188_aquaporin_Z_1453266..1453416_POSITIVE 156 97 55 123 80 smit:SMT_1950|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_1885069..1885219_POSITIVE 156 93 55 43 1 smit:SMT_794|3end_hypothetical_protein_703245..703395_NEGATIVE 154 100 56 124 69 smit:SMT_1133|3end_cytidine/deoxycytidylate_deaminase_family_protein,_putative_1074556..1074706_NEGATIVE 152 50 1 124 75 smit:SMT_393|3end_hypothetical_protein_predicted_by_Glimmer/Critica_324193..324343_POSITIVE 143 100 74 33 6 smit:SMT_1544|3end_mevalonate_kinase_1528006..1528156_NEGATIVE 141 93 56 70 46 smit:SMT_466|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_404342..404492_POSITIVE 140 99 66 138 101 smit:SMT_208|3end_leucyl-tRNA_synthetase_142558..142708_POSITIVE 139 89 47 136 100 smit:SMT_814|3end_UDP-N-acetyl_muramate-alanine_ligase_722332..722482_NEGATIVE 138 20 1 61 42 smit:SMT_2022|3end_hypothetical_protein_1938993..1939143_POSITIVE 137 98 57 70 36 smit:SMT_1350|3end_multidrug_resistance_efflux_pump_1328026..1328176_NEGATIVE 137 94 64 42 15 smit:SMT_620|3end_hypothetical_protein_predicted_by_Glimmer/Critica_528971..529121_POSITIVE 136 100 58 86 42 smit:SMT_1756|3end_hypothetical_protein_1733967..1734117_NEGATIVE 135 91 64 26 5 smit:SMT_1879|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836567..1836717_NEGATIVE 134 93 55 130 88 smit:SMT_1375|3end_putative_glucose-inhibited_division_protein_1353104..1353254_NEGATIVE