Origin IGS: gaaacctgaaaatgtgaaaaagacatctaccccgaaaaatctcctggaagatgggtctgaagagtgatacagagtaccaaagtaacctggtatcctatcaaggaaacatttatgnnnnnttaattaattaannnnnaaaagtaaacctgtaatcctaatcaaggaaaaccatttaatgcgcatacgagtttattcttcctttcattgtacactttattctatcaaaaaaagaagaaaaatcctaagagaaaacttaggatttttagcttatatcaattccagt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 actggaattgatataagctaaaaatcctaagttttctcttaggatttttcttctttttttgatagaataaagtgtacaatgaaaggaagaataaactcgtatgcgcattaaatggttttccttgattaggattacaggtttacttttnnnnnttaattaattaannnnncataaatgtttccttgataggataccaggttactttggtactctgtatcactcttcagacccatcttccaggagatttttcggggtagatgtctttttcacattttcaggtttc Mask Tandem Repeat Region ================================================ gaaacctgaaaatgtgaaaaagacatctaccccgaaaaatctcctggaagatgggtctgaagagtgatacagagtaccaaagtaacctggtatcctatcaaggaaacatttatgnnnnnttaattaattaannnnnaaaagtaaacctgtaatcctaatcaaggaaaaccatttaatgcgcatacgagtttattcttcctttcattgtacactttattctatcaaaaaaagaagaaaaatcctaagagaaaacttaggatttttagcttatatcaattccagt Find is-nt database================================================ Query_seq: SMT_1121:SMT_1122|SMT_1121:SMT_1122:hypothetical protein:queuine tRNA-ribosyltransferase:<-<-:1057888..1058170 283 gaaacctgaaaatgtgaaaaagacatctaccccgaaaaatctcctggaagatgggtctgaagagtgatacagagtaccaaagtaacctggtatcctatcaaggaaacatttatgnnnnnttaattaattaannnnnaaaagtaaacctgtaatcctaatcaaggaaaaccatttaatgcgcatacgagtttattcttcctttcattgtacactttattctatcaaaaaaagaagaaaaatcctaagagaaaacttaggatttttagcttatatcaattccagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1121:SMT_1122|SMT_1121:SMT_1122:hypothetical protein:queuine tRNA-ribosyltransferase:<-<-:1057888..1058170 283 gaaacctgaaaatgtgaaaaagacatctaccccgaaaaatctcctggaagatgggtctgaagagtgatacagagtaccaaagtaacctggtatcctatcaaggaaacatttatgnnnnnttaattaattaannnnnaaaagtaaacctgtaatcctaatcaaggaaaaccatttaatgcgcatacgagtttattcttcctttcattgtacactttattctatcaaaaaaagaagaaaaatcctaagagaaaacttaggatttttagcttatatcaattccagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1121:SMT_1122|SMT_1121:SMT_1122:hypothetical protein:queuine tRNA-ribosyltransferase:<-<-:1057888..1058170 283 gaaacctgaaaatgtgaaaaagacatctaccccgaaaaatctcctggaagatgggtctgaagagtgatacagagtaccaaagtaacctggtatcctatcaaggaaacatttatgnnnnnttaattaattaannnnnaaaagtaaacctgtaatcctaatcaaggaaaaccatttaatgcgcatacgagtttattcttcctttcattgtacactttattctatcaaaaaaagaagaaaaatcctaagagaaaacttaggatttttagcttatatcaattccagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaacctgaaaatgtgaaaaagacatctaccccgaaaaatctcctggaagatgggtctgaagagtgatacagagtaccaaagtaacctggtatcctatcaaggaaacatttatgnnnnnttaattaattaannnnnaaaagtaaacctgtaatcctaatcaaggaaaaccatttaatgcgcatacgagtttattcttcctttcattgtacactttattctatcaaaaaaagaagaaaaatcctaagagaaaacttaggatttttagcttatatcaattccagt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 39 End: 128 ...................................... M S W K M G L K S D T E Y Q S N L V S Y Q G N I Y X X L I N ........................................................................................................................................................... Protein_Len: 44 Strand: + Start: 152 End: 283 ....................................................................................................................................................... M L I K E N H L M R I R V Y S S F H C T L Y S I K K R R K I L R E N L G F L A Y I N S S Protein_Len: 31 Strand: - Start: 1 End: 93 F G S F T F F V D V G F F R R S S P D S S H Y L T G F Y G P M .............................................................................................................................................................................................. gaaacctgaaaatgtgaaaaagacatctaccccgaaaaatctcctggaagatgggtctgaagagtgatacagagtaccaaagtaacctggtatcctatcaaggaaacatttatgnnnnnttaattaattaannnnnaaaagtaaacctgtaatcctaatcaaggaaaaccatttaatgcgcatacgagtttattcttcctttcattgtacactttattctatcaaaaaaagaagaaaaatcctaagagaaaacttaggatttttagcttatatcaattccagt 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================================================ gaaacctgaaaatgtgaaaaagacatctaccccgaaaaatctcctggaagatgggtctgaagagtgatacagagtaccaaagtaacctggtatcctatcaaggaaacatttatgnnnnnttaattaattaannnnnaaaagtaaacctgtaatcctaatcaaggaaaaccatttaatgcgcatacgagtttattcttcctttcattgtacactttattctatcaaaaaaagaagaaaaatcctaagagaaaacttaggatttttagcttatatcaattccagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -6.5 Tail_Score: -4.79756 Start: 240 End: 259 Full_Region: AAAAAAGAAGAAAAA TCCTAAG AGAAAA CTTAGGA TTTTTAGCTTATATC ...............................................................................................................................................................................................................................................TCCTAAGAGAAAACTTAGGA........................ Find igs database================================================ Query_seq: SMT_1121:SMT_1122|SMT_1121:SMT_1122:hypothetical protein:queuine tRNA-ribosyltransferase:<-<-:1057888..1058170 283 gaaacctgaaaatgtgaaaaagacatctaccccgaaaaatctcctggaagatgggtctgaagagtgatacagagtaccaaagtaacctggtatcctatcaaggaaacatttatgnnnnnttaattaattaannnnnaaaagtaaacctgtaatcctaatcaaggaaaaccatttaatgcgcatacgagtttattcttcctttcattgtacactttattctatcaaaaaaagaagaaaaatcctaagagaaaacttaggatttttagcttatatcaattccagt Intra-Species Hit: Count: 1 Min: 1 Max: 283 Len: 283 Subject: smit_SMT_1121_SMT_1122|hypothetical protein:queuine tRNA-ribosyltransferase|NEGATIVE:NEGATIVE|[1057888, 1058170]|283 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 283 Query Start:1 Query End:283 Subject Strand: POSITIVE Subject Start: 1 Subject End: 283 gaaacctgaaaatgtgaaaaagacatctaccccgaaaaatctcctggaagatgggtctgaagagtgatacagagtaccaaagtaacctggtatcctatcaaggaaacatttatgnnnnnttaattaattaannnnnaaaagtaaacctgtaatcctaatcaaggaaaaccatttaatgcgcatacgagtttattcttcctttcattgtacactttattctatcnnnnnnngaagaaaaatcctaagagaaaacttaggatttttagcttatatcaattccagt gaaacctgaaaatgtgaaaaagacatctaccccgaaaaatctcctggaagatgggtctgaagagtgatacagagtaccaaagtaacctggtatcctatcaaggaaacatttatgnnnnnttaattaattaannnnnaaaagtaaacctgtaatcctaatcaaggaaaaccatttaatgcgcatacgagtttattcttcctttcattgtacactttattctatcaaaaaaagaagaaaaatcctaagagaaaacttaggatttttagcttatatcaattccagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAACCUGAAAAUGUGAAAAAGACAUCUACCCCGAAAAAUCUCCUGGAAGAUGGGUCUGAAGAGUGAUACAGAGUACCAAAGUAACCUGGUAUCCUAUCAAGGAAACAUUUAUGNNNNNUUAAUUAAUUAANNNNNAAAAGUAAACCUGUAAUCCUAAUCAAGGAAAACCAUUUAAUGCGCAUACGAGUUUAUUCUUCCUUUCAUUGUACACUUUAUUCUAUCAAAAAAAGAAGAAAAAUCCUAAGAGAAAACUUAGGAUUUUUAGCUUAUAUCAAUUCCAGU ...........((((.......)))).................((((((((((((.....((((((.(((((.((((((........))))))......((((((....(((........)))................(((((((.((((.((((.....))))....(((...)))....)))).))))))).))))))...)))))))))))..)))))).....(((...((((((((((((......))))))))))))..))).......)))))). (-52.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGGAAUUGAUAUAAGCUAAAAAUCCUAAGUUUUCUCUUAGGAUUUUUCUUCUUUUUUUGAUAGAAUAAAGUGUACAAUGAAAGGAAGAAUAAACUCGUAUGCGCAUUAAAUGGUUUUCCUUGAUUAGGAUUACAGGUUUACUUUUNNNNNUUAAUUAAUUAANNNNNCAUAAAUGUUUCCUUGAUAGGAUACCAGGUUACUUUGGUACUCUGUAUCACUCUUCAGACCCAUCUUCCAGGAGAUUUUUCGGGGUAGAUGUCUUUUUCACAUUUUCAGGUUUC .((((((.((......((..(((((((((((......)))))))))))((((((((((((((((........))).))).))))))))))..............))..(((((.((..((((.....))))..))..)))))................................(((((((((((((((..(((((((....)))))))..))).....(((((.(((....)))...))))).....)))))).))))))........)).))))))..... (-58.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 962 90 41 181 132 smit:SMT_1121|5end_hypothetical_protein_1057797..1058027_NEGATIVE 299 59 11 87 29 smit:SMT_1783|5end_peptide_methionine_sulfoxide_reductase_1759756..1759986_POSITIVE 296 68 21 150 95 smit:SMT_342|5end_chaperone_protein_DnaJ_281800..282030_POSITIVE 290 219 177 197 154 smit:SMT_1291|5end_hypothetical_protein_1253875..1254105_POSITIVE 289 90 41 145 96 smit:SMT_1005|5end_possible_aluminum_resistance_protein_945946..946176_POSITIVE 281 80 32 225 157 smit:SMT_948|5end_hypothetical_protein_predicted_by_Glimmer/Critica_896756..896986_NEGATIVE 278 80 33 218 178 smit:SMT_1032|5end_putative_biotin_operon_repressor_968744..968974_POSITIVE 274 208 175 218 180 smit:SMT_1292|5end_K02050_sulfonate/nitrate/taurine_transport_system_permease_protein_1254179..1254409_POSITIVE 272 50 4 67 20 smit:SMT_2128|5end_cell_division_protein_FtsA_2009617..2009847_POSITIVE 272 80 45 39 5 smit:SMT_1423|5end_hypothetical_protein_1407737..1407967_POSITIVE 270 100 52 72 14 smit:SMT_607|5end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520119..520349_POSITIVE 269 106 61 52 7 smit:SMT_117|5end_K02025_multiple_sugar_transport_system_permease_protein_68487..68717_POSITIVE 262 90 44 167 128 smit:SMT_1218|5end_DNA_polymerase_I_1179357..1179587_NEGATIVE 257 80 31 72 21 smit:SMT_211|5end_hypothetical_protein_predicted_by_Glimmer/Critica_144135..144365_POSITIVE 256 79 31 229 182 smit:SMT_839|5end_ABC_transporter,_ATP-binding_protein_786065..786295_NEGATIVE 256 68 21 52 9 smit:SMT_597|5end_K08974_putative_membrane_protein_513917..514147_NEGATIVE 252 199 153 75 29 smit:SMT_1350|5end_multidrug_resistance_efflux_pump_1329225..1329455_NEGATIVE 252 78 33 212 156 smit:SMT_1029|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_965632..965862_NEGATIVE 252 90 45 64 22 smit:SMT_128|5end_K03449_MFS_transporter,_CP_family,_cyanate_transporter_79868..80098_NEGATIVE 249 90 43 225 185 smit:SMT_1066|5end_holo-(acyl_carrier_protein)_synthase_1005411..1005641_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 70 26 148 102 smit:SMT_1682|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_1666373..1666523_POSITIVE 256 75 33 88 55 smit:SMT_594|3end_lysyl-tRNA_synthetase_510348..510498_NEGATIVE 253 57 19 147 110 smit:SMT_804|3end_S-adenosylmethionine_synthetase_713884..714034_NEGATIVE 252 199 153 88 42 smit:SMT_1351|3end_dephospho-CoA_kinase_1329212..1329362_NEGATIVE 249 59 13 147 89 smit:SMT_580|3end_K04094_glucose_inhibited_division_protein_Gid_498034..498184_POSITIVE 244 80 31 139 96 smit:SMT_1265|3end_hypothetical_protein_1230872..1231022_NEGATIVE 241 205 162 107 65 smit:SMT_449|3end_hypothetical_protein_388219..388369_POSITIVE 237 88 43 82 46 smit:SMT_1795|3end_DNA_polymerase_III,_delta_subunit_1769185..1769335_NEGATIVE 236 210 175 48 16 smit:SMT_197|3end_DNA-directed_RNA_polymerase,_alpha_subunit_128467..128617_POSITIVE 235 45 16 98 68 smit:SMT_977|3end_conserved_hypothetical_protein,_Rrf2_family_protein_925252..925402_NEGATIVE 235 73 42 85 49 smit:SMT_882|3end_acetyl_esterase_829662..829812_NEGATIVE 234 104 62 88 45 smit:SMT_772|3end_spermidine/putrescine_ABC_transporter,_ATP-binding_protein_682143..682293_NEGATIVE 233 87 48 67 24 smit:SMT_1423|3end_hypothetical_protein_1409811..1409961_POSITIVE 232 55 26 142 115 smit:SMT_1030|3end_alpha-galactosidase_965667..965817_NEGATIVE 231 80 32 61 1 smit:SMT_627|3end_glucose-1-phosphate_adenylyltransferase_532921..533071_POSITIVE 231 77 32 46 7 smit:SMT_198|3end_50S_ribosomal_protein_L17_129281..129431_POSITIVE 230 97 52 118 57 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 229 60 13 58 4 smit:SMT_1071|3end_hypothetical_protein_1010386..1010536_POSITIVE 229 59 15 121 75 smit:SMT_702|3end_hypothetical_protein_611946..612096_NEGATIVE 228 90 44 75 38 smit:SMT_1701|3end_transcriptional_regulator,_RpiR_family_1683599..1683749_NEGATIVE