Origin IGS: gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa .........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 tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc Mask Tandem Repeat Region ================================================ gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa Find is-nt database================================================ Query_seq: SMT_200:SMT_201|SMT_200:SMT_201:hypothetical protein:phosphoglycerate mutase:->->:131225..131468 244 gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_200:SMT_201|SMT_200:SMT_201:hypothetical protein:phosphoglycerate mutase:->->:131225..131468 244 gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_200:SMT_201|SMT_200:SMT_201:hypothetical protein:phosphoglycerate mutase:->->:131225..131468 244 gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 126 End: 218 ............................................................................................................................. M S L F N R T P K L F H N N L L Q K S P V W V A F V L S S M I .......................... Protein_Len: 35 Strand: - Start: 31 End: 135 .............................. P Q I H I S Y D N F L S R R I N N S V S L V S K T Q I Q N E D L I K M ............................................................................................................. Protein_Len: 32 Strand: - Start: 27 End: 122 .......................... K L N S T Y V I I M L Y L G G L I I Q F L Y C Q N L K F K I K M .......................................................................................................................... gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa 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================================================ gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -11.4 Tail_Score: -4.4767 Start: 174 End: 201 Full_Region: CATAATAATCTCCTG CAAAAGTCACCT GTCT GGGTGGCTTTTG TTTTATCATCCATGA .............................................................................................................................................................................CAAAAGTCACCTGTCTGGGTGGCTTTTG........................................... TransTerm Strand: + Conf: 81 HP_score: -5.5 Tail_Score: -5.20781 Start: 179 End: 196 Full_Region: TAATCTCCTGCAAAA GTCACCT GTCT GGGTGGC TTTTGTTTTATCATC ..................................................................................................................................................................................GTCACCTGTCTGGGTGGC................................................ Find igs database================================================ Query_seq: SMT_200:SMT_201|SMT_200:SMT_201:hypothetical protein:phosphoglycerate mutase:->->:131225..131468 244 gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa Intra-Species Hit: Count: 3 Min: 1 Max: 244 Len: 244 Subject: smit_SMT_2062_SMT_2063|phosphoglycerate mutase:hypothetical protein|NEGATIVE:NEGATIVE|[1971516,1971759]|244 HSP 1 e-value: 1.0E-136 bit: 484.0 Len: 244 Query Start:1 Query End:244 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 244 gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa Subject: smit_SMT_1995_SMT_1996|phosphoglycerate mutase:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:NEGATIVE|[1920841,1921084]|244 HSP 1 e-value: 1.0E-136 bit: 484.0 Len: 244 Query Start:1 Query End:244 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 244 gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa Subject: smit_SMT_200_SMT_201|hypothetical protein:phosphoglycerate mutase|POSITIVE:POSITIVE|[131225,131468]|244 HSP 1 e-value: 1.0E-136 bit: 484.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1 Subject End: 244 gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa Inter-species Hit: Count: 3 Min: 1 Max: 244 Len: 244 Subject: NC_008533_SPD_0220_SPD_0222|hypothetical protein:phosphoglycerate mutase family protein|POSITIVE:POSITIVE|[210876,212466]|1591 HSP 1 e-value: 1.0E-112 bit: 404.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1349 Subject End: 1591 gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa gaaaataggagaaattttaagttctatttaagattagatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgaattagtttgaatttgattttcatctaatatctttatttaat-gaactcctaaactttttcataataatctccttcaaaagtcgcctgtatgggtggcttttattttatcattcatgatataatagaagcaaacggaggacggaaa Subject: NC_003028_SP_0239_SP_0240|hypothetical protein:phosphoglycerate mutase family protein|POSITIVE:POSITIVE|[209714,209956]|243 HSP 1 e-value: 1.0E-109 bit: 396.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1 Subject End: 243 gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa gaaaataggagaaattttaagttctatttaagattagacgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgaattagtttgaatttgattttcatctaatatctttatttaat-gaactcctaaactttttcataataatctccttcaaaagtcgcctgtatgggtggcttttattttatcattcatgatataatagaagcaaacggaggacggaaa Subject: NC_003098_spr0218_spr0219|hypothetical protein:Phosphoglycerate mutase 2 paralog|POSITIVE:POSITIVE|[212223,212408]|186 HSP 1 e-value: 4.0E-85 bit: 315.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 186 gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgt......................................................... gaaaataggagaaattttaagttctatttaagattagatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgaattagtttgaatttgattttcatctaatatctttatttaat-gaactcctaaactttttcataataatctccttcaaaagtcgcctgt......................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAUAGGAGAAAUUUUAAGUUCUAUUUAAGGUUGGAUGUGUAUACUAUAAUCAUUAAAUAAAGACCUCCUAAUAUUAUUUGAAACAGAUAACACUGAUUUAGUUUGAAUUUGAUUUUCAUCUAAUAUCUUUAUUUAAUAGAACUCCUAAACUUUUUCAUAAUAAUCUCCUGCAAAAGUCACCUGUCUGGGUGGCUUUUGUUUUAUCAUCCAUGAUAUAAUAGAAGCAAACGGAGGACGGAAA (((((((((((.((((((((((...)))))))))).................((((((((((((((..........(((((((...))))))).......((((..((((.......)))).))))..)))))))))))).)).))))))....))))).......(((((.(((((((((((((....)))))))))))))..(((((....)))))..............)))))....... (-54.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCCGUCCUCCGUUUGCUUCUAUUAUAUCAUGGAUGAUAAAACAAAAGCCACCCAGACAGGUGACUUUUGCAGGAGAUUAUUAUGAAAAAGUUUAGGAGUUCUAUUAAAUAAAGAUAUUAGAUGAAAAUCAAAUUCAAACUAAAUCAGUGUUAUCUGUUUCAAAUAAUAUUAGGAGGUCUUUAUUUAAUGAUUAUAGUAUACACAUCCAACCUUAAAUAGAACUUAAAAUUUCUCCUAUUUUC .....(((.(((((................))))).)))....((((((.((((......)))).)))))).((((((.............(((((((.(((.((((((((((((((....(((....)))................((((((((.((...)).)))))))).....))))))))))))))......((....))....)))))))))).............))))))...... (-45.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 206 168 176 142 smit:SMT_700|5end_putative_signal_recognition_particle_-inhibited_division_protein_611511..611741_NEGATIVE 320 201 175 153 127 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 320 201 175 153 127 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 317 215 176 209 156 smit:SMT_1188|5end_hypothetical_protein_1146653..1146883_NEGATIVE 297 204 167 143 101 smit:SMT_1212|5end_acyl_carrier_protein,_putative_1171657..1171887_NEGATIVE 296 218 179 140 94 smit:SMT_190|5end_preprotein_translocase,_SecY_subunit_124285..124515_POSITIVE 286 200 151 192 144 smit:SMT_1890|5end_hypothetical_protein_1843407..1843637_POSITIVE 284 214 178 58 21 smit:SMT_805|5end_hypothetical_protein_predicted_by_Glimmer/Critica_715793..716023_NEGATIVE 280 196 152 183 121 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 276 200 154 125 84 smit:SMT_1788|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1765029..1765259_NEGATIVE 276 200 154 125 84 smit:SMT_1197|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1158751..1158981_NEGATIVE 271 218 171 62 14 smit:SMT_2134|5end_hypothetical_protein_2014700..2014930_NEGATIVE 271 218 171 62 14 smit:SMT_873|5end_hypothetical_protein_821311..821541_NEGATIVE 264 185 141 135 82 smit:SMT_355|5end_hypothetical_protein_291622..291852_POSITIVE 263 228 184 141 95 smit:SMT_2062|5end_phosphoglycerate_mutase_1971425..1971655_NEGATIVE 263 228 184 141 95 smit:SMT_1995|5end_phosphoglycerate_mutase_1920750..1920980_NEGATIVE 263 203 163 71 29 smit:SMT_78|5end_tryptophanyl-tRNA_synthetase_6531..6761_NEGATIVE 262 220 171 157 104 smit:SMT_487|5end_transcriptional_regulator,_TetR_family_422380..422610_POSITIVE 261 195 152 205 158 smit:SMT_1170|5end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1118126..1118356_NEGATIVE 258 220 171 92 38 smit:SMT_2034|5end_hydrolase,_haloacid_dehalogenase-like_family_1946671..1946901_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 204 167 137 95 smit:SMT_1213|3end_fatty_acid/phospholipid_synthesis_protein_PlsX_1171663..1171813_NEGATIVE 296 218 179 127 81 smit:SMT_189|3end_50S_ribosomal_protein_L15_124352..124502_POSITIVE 264 185 141 104 51 smit:SMT_354|3end_hypothetical_protein_291671..291821_POSITIVE 261 195 152 109 62 smit:SMT_1171|3end_hypothetical_protein_1118222..1118372_NEGATIVE 258 220 171 80 26 smit:SMT_2033|3end_hydrolase,_haloacid_dehalogenase-like_family_1946739..1946889_POSITIVE 258 210 167 41 5 smit:SMT_355|3end_hypothetical_protein_292313..292463_POSITIVE 256 203 162 151 98 smit:SMT_805|3end_hypothetical_protein_predicted_by_Glimmer/Critica_715692..715842_NEGATIVE 253 149 113 107 74 smit:SMT_707|3end_hypothetical_protein_predicted_by_Glimmer/Critica_616239..616389_NEGATIVE 248 209 170 36 3 smit:SMT_1104|3end_K06346_spoIIIJ-associated_protein_1045795..1045945_NEGATIVE 248 201 171 140 105 smit:SMT_678|3end_K04096_DNA_processing_protein_587447..587597_NEGATIVE 243 220 171 150 105 smit:SMT_2045|3end_K+_transport_system,_NAD-binding_component_1956758..1956908_POSITIVE 243 220 171 150 105 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 243 195 168 75 32 smit:SMT_458|3end_hypothetical_protein_predicted_by_Glimmer/Critica_396729..396879_NEGATIVE 242 213 171 137 96 smit:SMT_801|3end_glycyl-tRNA_synthetase_alpha_chain_709892..710042_NEGATIVE 241 206 172 71 33 smit:SMT_1383|3end_ribonucleoside-diphosphate_reductase_alpha_chain_1360795..1360945_NEGATIVE 240 120 82 79 50 smit:SMT_456|3end_pyruvate_oxidase_396091..396241_POSITIVE 239 195 175 75 51 smit:SMT_1541|3end_isopentenyl-diphosphate_delta-isomerase_1525083..1525233_NEGATIVE 238 203 167 74 33 smit:SMT_628|3end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_534050..534200_POSITIVE 236 190 144 139 84 smit:SMT_977|3end_conserved_hypothetical_protein,_Rrf2_family_protein_925252..925402_NEGATIVE 236 201 170 75 41 smit:SMT_521|3end_K02005_HlyD_family_secretion_protein_446815..446965_POSITIVE