Origin IGS: agaaactacagaaccttcttgaatagcaccttctgtaactgtaagttctaactcagttggtgagattaatctaggtgttagtgtgaacccactatcacgaccatcgtttagaatccaaacgttgttttcgttagctttaacattagcccatcgactagctggacgatatgtaatactatctcctttattagggttaatagtggacgctgtatttaatccatttacaaagttagaacttccttcaagttctttaaactcagtaaaatctgcattggnnnnnttaattaattaannnnngacaaagcaccaacga .........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 tcgttggtgctttgtcnnnnnttaattaattaannnnnccaatgcagattttactgagtttaaagaacttgaaggaagttctaactttgtaaatggattaaatacagcgtccactattaaccctaataaaggagatagtattacatatcgtccagctagtcgatgggctaatgttaaagctaacgaaaacaacgtttggattctaaacgatggtcgtgatagtgggttcacactaacacctagattaatctcaccaactgagttagaacttacagttacagaaggtgctattcaagaaggttctgtagtttct Mask Tandem Repeat Region ================================================ agaaactacagaaccttcttgaatagcaccttctgtaactgtaagttctaactcagttggtgagattaatctaggtgttagtgtgaacccactatcacgaccatcgtttagaatccaaacgttgttttcgttagctttaacattagcccatcgactagctggacgatatgtaatactatctcctttattagggttaatagtggacgctgtatttaatccatttacaaagttagaacttccttcaagttctttaaactcagtaaaatctgcattggnnnnnttaattaattaannnnngacaaagcaccaacga Find is-nt database================================================ Query_seq: SMT_2090:SMT_2091|SMT_2090:SMT_2091:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:<-->:1986062..1986374 313 agaaactacagaaccttcttgaatagcaccttctgtaactgtaagttctaactcagttggtgagattaatctaggtgttagtgtgaacccactatcacgaccatcgtttagaatccaaacgttgttttcgttagctttaacattagcccatcgactagctggacgatatgtaatactatctcctttattagggttaatagtggacgctgtatttaatccatttacaaagttagaacttccttcaagttctttaaactcagtaaaatctgcattggnnnnnttaattaattaannnnngacaaagcaccaacga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2090:SMT_2091|SMT_2090:SMT_2091:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:<-->:1986062..1986374 313 agaaactacagaaccttcttgaatagcaccttctgtaactgtaagttctaactcagttggtgagattaatctaggtgttagtgtgaacccactatcacgaccatcgtttagaatccaaacgttgttttcgttagctttaacattagcccatcgactagctggacgatatgtaatactatctcctttattagggttaatagtggacgctgtatttaatccatttacaaagttagaacttccttcaagttctttaaactcagtaaaatctgcattggnnnnnttaattaattaannnnngacaaagcaccaacga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2090:SMT_2091|SMT_2090:SMT_2091:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:<-->:1986062..1986374 313 agaaactacagaaccttcttgaatagcaccttctgtaactgtaagttctaactcagttggtgagattaatctaggtgttagtgtgaacccactatcacgaccatcgtttagaatccaaacgttgttttcgttagctttaacattagcccatcgactagctggacgatatgtaatactatctcctttattagggttaatagtggacgctgtatttaatccatttacaaagttagaacttccttcaagttctttaaactcagtaaaatctgcattggnnnnnttaattaattaannnnngacaaagcaccaacga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaactacagaaccttcttgaatagcaccttctgtaactgtaagttctaactcagttggtgagattaatctaggtgttagtgtgaacccactatcacgaccatcgtttagaatccaaacgttgttttcgttagctttaacattagcccatcgactagctggacgatatgtaatactatctcctttattagggttaatagtggacgctgtatttaatccatttacaaagttagaacttccttcaagttctttaaactcagtaaaatctgcattggnnnnnttaattaattaannnnngacaaagcaccaacga Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 23 End: 289 ...................... M A P S V T V S S N S V G E I N L G V S V N P L S R P S F R I Q T L F S L A L T L A H R L A G R Y V I L S P L L G L I V ........................ Protein_Len: 34 Strand: - Start: 111 End: 212 .............................................................................................................. F G F T T K T L K L M L G D V L Q V I H L V I E K I L T L L P R Q M ..................................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 285 N L I W V N N E N A K V N A W R S A P R Y T I S D G K N P N I T S A T N L G N V F N S S G E L E K F E T F D A N X X X M ............................ agaaactacagaaccttcttgaatagcaccttctgtaactgtaagttctaactcagttggtgagattaatctaggtgttagtgtgaacccactatcacgaccatcgtttagaatccaaacgttgttttcgttagctttaacattagcccatcgactagctggacgatatgtaatactatctcctttattagggttaatagtggacgctgtatttaatccatttacaaagttagaacttccttcaagttctttaaactcagtaaaatctgcattggnnnnnttaattaattaannnnngacaaagcaccaacga 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================================================ agaaactacagaaccttcttgaatagcaccttctgtaactgtaagttctaactcagttggtgagattaatctaggtgttagtgtgaacccactatcacgaccatcgtttagaatccaaacgttgttttcgttagctttaacattagcccatcgactagctggacgatatgtaatactatctcctttattagggttaatagtggacgctgtatttaatccatttacaaagttagaacttccttcaagttctttaaactcagtaaaatctgcattggnnnnnttaattaattaannnnngacaaagcaccaacga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -5.2 Tail_Score: -3.61178 Start: 233 End: 249 Full_Region: CCATTTACAAAGTTA GAACTT CCTTC AAGTTC TTTAAACTCAGTAAA ........................................................................................................................................................................................................................................GAACTTCCTTCAAGTTC................................................................ TransTerm Strand: - Conf: 49 HP_score: -5.2 Tail_Score: -2.71325 Start: 233 End: 249 Full_Region: tttactgagtttaaa gaactt gaagg aagttc taactttgtaaatgg ........................................................................................................................................................................................................................................gaacttgaaggaagttc................................................................ Find igs database================================================ Query_seq: SMT_2090:SMT_2091|SMT_2090:SMT_2091:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:<-->:1986062..1986374 313 agaaactacagaaccttcttgaatagcaccttctgtaactgtaagttctaactcagttggtgagattaatctaggtgttagtgtgaacccactatcacgaccatcgtttagaatccaaacgttgttttcgttagctttaacattagcccatcgactagctggacgatatgtaatactatctcctttattagggttaatagtggacgctgtatttaatccatttacaaagttagaacttccttcaagttctttaaactcagtaaaatctgcattggnnnnnttaattaattaannnnngacaaagcaccaacga Intra-Species Hit: Count: 1 Min: 1 Max: 313 Len: 313 Subject: smit_SMT_2090_SMT_2091|hypothetical protein predicted by Glimmer/Critica:hypothetical protein|NEGATIVE:POSITIVE|[1986062,1986374]|313 HSP 1 e-value: 1.0E-155 bit: 549.0 Len: 313 Query Start:1 Query End:313 Subject Strand: POSITIVE Subject Start: 1 Subject End: 313 agaaactacagaaccttcttgaatagcaccttctgtaactgtaagttctaactcagttggtgagattaatctaggtgttagtgtgaacccactatcacgaccatcgtttagaatccaaacgttgttttcgttagctttaacattagcccatcgactagctggacgatatgtaatactatctcctttattagggttaatagtggacgctgtatttaatccatttacaaagttagaacttccttcaagttctttaaactcagtaaaatctgcattnnnnnnnttaattaattaannnnngacaaagcaccaacga agaaactacagaaccttcttgaatagcaccttctgtaactgtaagttctaactcagttggtgagattaatctaggtgttagtgtgaacccactatcacgaccatcgtttagaatccaaacgttgttttcgttagctttaacattagcccatcgactagctggacgatatgtaatactatctcctttattagggttaatagtggacgctgtatttaatccatttacaaagttagaacttccttcaagttctttaaactcagtaaaatctgcattggnnnnnttaattaattaannnnngacaaagcaccaacga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAACUACAGAACCUUCUUGAAUAGCACCUUCUGUAACUGUAAGUUCUAACUCAGUUGGUGAGAUUAAUCUAGGUGUUAGUGUGAACCCACUAUCACGACCAUCGUUUAGAAUCCAAACGUUGUUUUCGUUAGCUUUAACAUUAGCCCAUCGACUAGCUGGACGAUAUGUAAUACUAUCUCCUUUAUUAGGGUUAAUAGUGGACGCUGUAUUUAAUCCAUUUACAAAGUUAGAACUUCCUUCAAGUUCUUUAAACUCAGUAAAAUCUGCAUUGGNNNNNUUAAUUAAUUAANNNNNGACAAAGCACCAACGA ((((..(((((((....((.....))....)))))))...(.(((((((((((..((..(((.((((((....((((((..(((((........)))))...(((((((((......((((.......)))).(((........)))...........)))))))))......((((((..((((....))))...))))))))))))....)))))))))..))..))))))))))).)......)))).................(((.(((......((((....)))).......))).)))....... (-62.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGUUGGUGCUUUGUCNNNNNUUAAUUAAUUAANNNNNCCAAUGCAGAUUUUACUGAGUUUAAAGAACUUGAAGGAAGUUCUAACUUUGUAAAUGGAUUAAAUACAGCGUCCACUAUUAACCCUAAUAAAGGAGAUAGUAUUACAUAUCGUCCAGCUAGUCGAUGGGCUAAUGUUAAAGCUAACGAAAACAACGUUUGGAUUCUAAACGAUGGUCGUGAUAGUGGGUUCACACUAACACCUAGAUUAAUCUCACCAACUGAGUUAGAACUUACAGUUACAGAAGGUGCUAUUCAAGAAGGUUCUGUAGUUUCU ..(((((((........................................(((((.(((((...(((((((.....)))))))))))).))))).(((((((.....(..(((((((((.....(((((..(((((((........)))).)))...(((((....))))).)))))......((((...((.(((((((...))))))).)).)))))))))))))..)...(((.....))).)))))))))))))).((((....))))....((((((((....((.....))....))))))))..... (-66.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 907 120 71 211 162 smit:SMT_2090|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1985971..1986201_NEGATIVE 285 170 122 160 114 smit:SMT_2032|5end_hydrolase,_alpha/beta_fold_family_1946421..1946651_NEGATIVE 281 177 131 230 187 smit:SMT_1113|5end_hypothetical_protein_1052071..1052301_NEGATIVE 281 65 27 177 136 smit:SMT_1008|5end_hypothetical_protein_948021..948251_NEGATIVE 275 230 181 80 29 smit:SMT_490|5end_branched-chain_amino_acid_ABC_transporter,_permease_protein_424544..424774_POSITIVE 270 206 161 225 174 smit:SMT_1828|5end_PTS_system,_galactose-specific_IIC_component_1797668..1797898_POSITIVE 270 206 161 125 74 smit:SMT_1827|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1797568..1797798_POSITIVE 268 86 41 169 122 smit:SMT_529|5end_30S_ribosomal_protein_S16_452177..452407_POSITIVE 267 153 115 59 13 smit:SMT_1047|5end_chaperonin,_10_kDa_988090..988320_NEGATIVE 262 120 73 151 115 smit:SMT_1646|5end_3-isopropylmalate_dehydratase_large_subunit_1632011..1632241_POSITIVE 262 54 12 205 166 smit:SMT_877|5end_hypothetical_protein_824412..824642_NEGATIVE 261 165 122 118 70 smit:SMT_1850|5end_K01421_putative_membrane_protein_1815062..1815292_POSITIVE 261 59 15 198 148 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 260 120 72 128 69 smit:SMT_279|5end_glycosyl_transferase_CpsE_221100..221330_POSITIVE 259 118 74 186 132 smit:SMT_235|5end_hypothetical_protein_174081..174311_POSITIVE 258 65 23 167 118 smit:SMT_835|5end_polypeptide_deformylase_777549..777779_NEGATIVE 258 40 1 79 38 smit:SMT_303|5end_hypothetical_protein_245364..245594_POSITIVE 257 126 84 218 179 smit:SMT_1168|5end_potassium_uptake_protein_KtrB_1116552..1116782_NEGATIVE 257 159 115 98 52 smit:SMT_1045|5end_cochaperonin_GroES_987582..987812_NEGATIVE 256 99 51 219 172 smit:SMT_1868|5end_thymidine_kinase_1828775..1829005_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 168 129 145 108 smit:SMT_862|3end_hypothetical_protein_predicted_by_Glimmer/Critica_809191..809341_POSITIVE 275 115 71 144 104 smit:SMT_798|3end_hypothetical_protein_707106..707256_POSITIVE 270 206 161 99 48 smit:SMT_1826|3end_ATP_synthase_beta_chain_1797622..1797772_POSITIVE 269 186 150 81 49 smit:SMT_2112|3end_transcription-repair_coupling_factor_2000373..2000523_NEGATIVE 262 120 73 147 111 smit:SMT_1645|3end_hypothetical_protein_1632087..1632237_POSITIVE 258 65 23 52 3 smit:SMT_836|3end_cell_surface_protein_precursor_777664..777814_NEGATIVE 253 189 142 95 50 smit:SMT_1959|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1892967..1893117_POSITIVE 253 189 142 95 50 smit:SMT_286|3end_polysaccharide_transporter,_PST_family_230150..230300_POSITIVE 245 170 121 109 52 smit:SMT_2014|3end_tryptophan_synthase_beta_chain_1932727..1932877_POSITIVE 245 184 144 140 107 smit:SMT_424|3end_transcriptional_regulatory_protein_368108..368258_POSITIVE 243 64 34 77 47 smit:SMT_1840|3end_6-phosphogluconate_dehydrogenase,_decarboxylating_1806007..1806157_NEGATIVE 241 106 64 133 85 smit:SMT_306|3end_3-oxoacyl-_249117..249267_POSITIVE 240 163 121 130 72 smit:SMT_1043|3end_chaperonin_GroEL_985110..985260_NEGATIVE 238 37 13 145 124 smit:SMT_1756|3end_hypothetical_protein_1733967..1734117_NEGATIVE 236 169 133 74 21 smit:SMT_280|3end_polysaccharide_biosynthesis_protein/putative_rhamnosyl_transferase_223628..223778_POSITIVE 235 65 22 133 77 smit:SMT_591|3end_K02029_polar_amino_acid_transport_system_permease_protein_508829..508979_POSITIVE 235 153 121 140 104 smit:SMT_213|3end_leucyl-tRNA_synthetase_146167..146317_POSITIVE 234 49 4 68 20 smit:SMT_2088|3end_glucose-1-phosphate_thymidylyltransferase_1985066..1985216_POSITIVE 234 190 147 56 10 smit:SMT_1682|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_1666373..1666523_POSITIVE 234 157 119 46 1 smit:SMT_1539|3end_sensor_histidine_kinase,_putative_1523315..1523465_NEGATIVE