Origin IGS: gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgaaaaaaactctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttagttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caactaaaccccctttttatctttgctatcattatatcattttttctcaagtaagggcttacctgtattgaaaaatagagtttttttcgataaaataggagacagttattttttaatagattagaaataggagaaatc Mask Tandem Repeat Region ================================================ gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgaaaaaaactctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttagttg Find is-nt database================================================ Query_seq: SMT_326:SMT_327|SMT_326:SMT_327:K02029 polar amino acid transport system permease protein:hypothetical protein:<-->:263955..264092 138 gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgaaaaaaactctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttagttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_326:SMT_327|SMT_326:SMT_327:K02029 polar amino acid transport system permease protein:hypothetical protein:<-->:263955..264092 138 gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgaaaaaaactctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttagttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_326:SMT_327|SMT_326:SMT_327:K02029 polar amino acid transport system permease protein:hypothetical protein:<-->:263955..264092 138 gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgaaaaaaactctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttagttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgaaaaaaactctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttagttg Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 2 End: 136 . M S P I S N L L K N N C L L F Y R K K L Y F S I Q V S P Y L R K N D I M I A K I K R G F S .. Protein_Len: 33 Strand: - Start: 18 End: 116 ................. D I L F Y S D G I K D F F V R N K L V P L G K S S F F H Y L S L M ...................... gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgaaaaaaactctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttagttg Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 90 Start: 43 End: 72 ..........................................ATTGAAAAATAGAGTTTTTTTCGATAAAAT.................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgaaaaaaactctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttagttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_326:SMT_327|SMT_326:SMT_327:K02029 polar amino acid transport system permease protein:hypothetical protein:<-->:263955..264092 138 gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgaaaaaaactctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttagttg Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: smit_SMT_326_SMT_327|K02029 polar amino acid transport system permease protein:hypothetical protein|NEGATIVE:POSITIVE|[263955,264092]|138 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgnnnnnnnctctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttagttg gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgaaaaaaactctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttagttg Inter-species Hit: Count: 3 Min: 1 Max: 138 Len: 138 Subject: NC_008533_SPD_0412_SPD_0414|amino acid ABC transporter, amino acid-binding protein/permease protein:hypothetical protein|NEGATIVE:POSITIVE|[413745,413881]|137 HSP 1 e-value: 4.0E-22 bit: 105.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgnnnnnnnctctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttagttg gatttctcctatt-ctgatctattaaaaaataactgtctcctattttatcgaaaaatgcgtaatttttcaacataagtaagcctttacttacgaaaaaatgctataatgataagaaagataaaaagggggcttagttg Subject: NC_003098_spr0409_spr0410|ABC transporter substrate binding protein - glutamine transport:hypothetical protein|NEGATIVE:POSITIVE|[405586,406349]|764 HSP 1 e-value: 2.0E-20 bit: 99.6 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 631 Subject End: 764 gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgnnnnnnnctctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttag... gatttctcctatt-ctgatctattaaaaaataactgtctcctattttatcgaaaaatgcgtaatttttcaacataagtaagcctttacttacgaaaaaatgctataatgataagaaagataaaaagggggcttag... Subject: NC_003028_SP_0453_SP_0454|amino acid ABC transporter, amino acid-binding protein/permease protein:hypothetical protein|NEGATIVE:POSITIVE|[426308,426441]|134 HSP 1 e-value: 6.0E-18 bit: 91.7 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 gatttctcctatttctaatctattaaaaaataactgtctcctattttatcgnnnnnnnctctatttttcaatacaggtaagcccttacttgagaaaaaatgatataatgatagcaaagataaaaagggggtttag... gatttctcctatt-ctgatctattaaaaaataactgtctcctattttatcgaaaaatgcgtaatttttcaacataagtaagtctttacttacgaaaaaatgctataatgataagaaagataaaaagggggcttag... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUCUCCUAUUUCUAAUCUAUUAAAAAAUAACUGUCUCCUAUUUUAUCGAAAAAAACUCUAUUUUUCAAUACAGGUAAGCCCUUACUUGAGAAAAAAUGAUAUAAUGAUAGCAAAGAUAAAAAGGGGGUUUAGUUG ..............................((((((.(((((.(((((((((((((.......))))))....(((((((....)))))))..........................))))))).)))))..)))))) (-23.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACUAAACCCCCUUUUUAUCUUUGCUAUCAUUAUAUCAUUUUUUCUCAAGUAAGGGCUUACCUGUAUUGAAAAAUAGAGUUUUUUUCGAUAAAAUAGGAGACAGUUAUUUUUUAAUAGAUUAGAAAUAGGAGAAAUC ..........................................((((((.....(((.....))).(((((((((((((.(((((((..........)))))))..)))))))))))))............)))))).. (-19.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 801 130 81 221 172 smit:SMT_326|5end_K02029_polar_amino_acid_transport_system_permease_protein_263864..264094_NEGATIVE 258 110 64 146 100 smit:SMT_1077|5end_GTP_cyclohydrolase_I_1015410..1015640_NEGATIVE 237 120 80 173 129 smit:SMT_399|5end_cytochrome_c-type_biogenesis_protein_CcdA_328366..328596_POSITIVE 233 130 90 189 148 smit:SMT_715|5end_DHH_subfamily_1_protein_621379..621609_POSITIVE 225 114 72 179 138 smit:SMT_1202|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1164097..1164327_NEGATIVE 214 50 5 137 91 smit:SMT_1826|5end_ATP_synthase_beta_chain_1797408..1797638_POSITIVE 214 50 5 137 91 smit:SMT_586|5end_ATP_synthase_F1,_beta_subunit_502533..502763_POSITIVE 214 130 82 145 94 smit:SMT_163|5end_cardiolipin_synthetase_107309..107539_POSITIVE 213 88 45 125 74 smit:SMT_355|5end_hypothetical_protein_291622..291852_POSITIVE 207 115 72 176 129 smit:SMT_1215|5end_aromatic_amino_acid_aminotransferase_1174588..1174818_NEGATIVE 206 129 81 206 159 smit:SMT_954|5end_cation-transporting_ATPase,_E1-E2_family_904025..904255_NEGATIVE 197 71 36 214 161 smit:SMT_300|5end_hypothetical_protein_243512..243742_POSITIVE 195 114 77 38 1 smit:SMT_1564|5end_transcriptional_antiterminator,_BglG_family_1555587..1555817_POSITIVE 191 50 3 140 96 smit:SMT_683|5end_similar_to_CDP-ribitol_pyrophosphorylase_592572..592802_NEGATIVE 189 77 31 49 5 smit:SMT_345|5end_K01990_ABC-2_type_transport_system_ATP-binding_protein_283992..284222_POSITIVE 184 78 35 171 127 smit:SMT_702|5end_hypothetical_protein_612311..612541_NEGATIVE 182 120 71 224 169 smit:SMT_856|5end_peroxide_resistance_protein,non-heme_iron-containing_ferritin_800648..800878_NEGATIVE 178 40 5 130 98 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 178 48 3 137 94 smit:SMT_368|5end_hypothetical_protein_303662..303892_POSITIVE 177 130 83 177 132 smit:SMT_1411|5end_ATP-dependent_nuclease_subunit_B_1395478..1395708_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 225 114 72 55 14 smit:SMT_1203|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1164221..1164371_NEGATIVE 214 50 5 51 5 smit:SMT_1825|3end_ATP_synthase_F1,_gamma_subunit_1797402..1797552_POSITIVE 214 50 5 51 5 smit:SMT_585|3end_ATP_synthase_gamma_chain_502527..502677_POSITIVE 213 88 45 94 43 smit:SMT_354|3end_hypothetical_protein_291671..291821_POSITIVE 203 91 60 147 117 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 181 110 76 144 104 smit:SMT_108|3end_hypothetical_protein_53873..54023_POSITIVE 179 101 82 78 60 smit:SMT_899|3end_5,10-methylenetetrahydrofolate_reductase_847397..847547_NEGATIVE 179 95 60 138 89 smit:SMT_357|3end_tRNA_(guanine-N7-)-methyltransferase_293900..294050_POSITIVE 178 40 5 133 101 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 178 48 3 127 84 smit:SMT_367|3end_hypothetical_protein_303732..303882_POSITIVE 173 88 42 137 95 smit:SMT_1911|3end_hypothetical_protein_1857840..1857990_POSITIVE 173 91 59 138 111 smit:SMT_896|3end_hypothetical_protein_843119..843269_NEGATIVE 173 88 42 137 95 smit:SMT_867|3end_hypothetical_protein_816542..816692_POSITIVE 173 47 2 129 73 smit:SMT_487|3end_transcriptional_regulator,_TetR_family_423017..423167_POSITIVE 168 96 60 139 98 smit:SMT_665|3end_NAD+_kinase_575927..576077_NEGATIVE 168 26 4 71 49 smit:SMT_508|3end_hypothetical_protein_438477..438627_NEGATIVE 168 103 75 72 48 smit:SMT_98|3end_hypothetical_protein_30272..30422_POSITIVE 167 91 59 134 89 smit:SMT_1118|3end_hypothetical_protein_1054779..1054929_NEGATIVE 166 93 59 123 89 smit:SMT_350|3end_immunity_protein_BlpL_290348..290498_POSITIVE 166 88 42 143 101 smit:SMT_123|3end_hypothetical_protein_75623..75773_POSITIVE