Origin IGS: acattttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgtttttttatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactattttggtaaaataaacttatgttataaaaactaacataaaggagaaagaag .........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 cttctttctcctttatgttagtttttataacataagtttattttaccaaaatagtgggaatttgtaaagttaattgaattttgagaatgaaagtttataaactttagtcataaaaaaacaaaggatttctgtctttcatacagtcctcccttgtttttatacgatttcaattttaaatttttctgtaaaaaatgt Mask Tandem Repeat Region ================================================ acattttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgtttttttatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactattttggtaaaataaacttatgttataaaaactaacataaaggagaaagaag Find is-nt database================================================ Query_seq: SMT_273:SMT_274|SMT_273:SMT_274:glucan 1,6-alpha-glucosidase:ABC transporter substrate-binding protein - oligopeptide transport:->->:215166..215360 195 acattttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgtttttttatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactattttggtaaaataaacttatgttataaaaactaacataaaggagaaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_273:SMT_274|SMT_273:SMT_274:glucan 1,6-alpha-glucosidase:ABC transporter substrate-binding protein - oligopeptide transport:->->:215166..215360 195 acattttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgtttttttatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactattttggtaaaataaacttatgttataaaaactaacataaaggagaaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_273:SMT_274|SMT_273:SMT_274:glucan 1,6-alpha-glucosidase:ABC transporter substrate-binding protein - oligopeptide transport:->->:215166..215360 195 acattttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgtttttttatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactattttggtaaaataaacttatgttataaaaactaacataaaggagaaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acattttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgtttttttatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactattttggtaaaataaacttatgttataaaaactaacataaaggagaaagaag Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 1 End: 99 C K K C F F K F N F D Y L F L P P S Y S L C F D K T K K H S F N M ................................................................................................ acattttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgtttttttatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactattttggtaaaataaacttatgttataaaaactaacataaaggagaaagaag 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: 89 Start: 127 End: 156 ..............................................................................................................................CTTTACAAATTCCCACTATTTTGGTAAAAT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acattttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgtttttttatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactattttggtaaaataaacttatgttataaaaactaacataaaggagaaagaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_273:SMT_274|SMT_273:SMT_274:glucan 1,6-alpha-glucosidase:ABC transporter substrate-binding protein - oligopeptide transport:->->:215166..215360 195 acattttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgtttttttatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactattttggtaaaataaacttatgttataaaaactaacataaaggagaaagaag Intra-Species Hit: Count: 1 Min: 1 Max: 195 Len: 195 Subject: smit_SMT_273_SMT_274|glucan 1,6-alpha-glucosidase:ABC transporter substrate-binding protein - oligopeptide transport|POSITIVE:POSITIVE|[215166,215360]|195 HSP 1 e-value: 3.0E-94 bit: 345.0 Len: 195 Query Start:1 Query End:195 Subject Strand: POSITIVE Subject Start: 1 Subject End: 195 acattttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgnnnnnnnatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactattttggtaaaataaacttatgttataaaaactaacataaaggagaaagaag acattttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgtttttttatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactattttggtaaaataaacttatgttataaaaactaacataaaggagaaagaag Inter-species Hit: Count: 2 Min: 3 Max: 146 Len: 144 Subject: NC_008533_SPD_0311_SPD_0313|glucan 1,6-alpha-glucosidase:hypothetical protein|POSITIVE:POSITIVE|[312324,312481]|158 HSP 1 e-value: 3.0E-39 bit: 163.0 Len: 144 Query Start:3 Query End:146 Subject Strand: POSITIVE Subject Start: 3 Subject End: 145 ..attttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgnnnnnnnatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactatt................................................. ..attttttgcagaaaaatttaaaattgaaatcatataaaaacaagggaggactgtataaaaagcagaaatcctttg-ttttttataaccaaagtttataaactttcattcttgaaattcaattaactttacaaattcccactatt................................................. Subject: NC_003098_spr0310_spr0311|Alpha, 1-6-glucosidase:hypothetical protein|POSITIVE:POSITIVE|[312275,312432]|158 HSP 1 e-value: 3.0E-39 bit: 163.0 Len: 144 Query Start:3 Query End:146 Subject Strand: POSITIVE Subject Start: 3 Subject End: 145 ..attttttacagaaaaatttaaaattgaaatcgtataaaaacaagggaggactgtatgaaagacagaaatcctttgnnnnnnnatgactaaagtttataaactttcattctcaaaattcaattaactttacaaattcccactatt................................................. ..attttttgcagaaaaatttaaaattgaaatcatataaaaacaagggaggactgtataaaaagcagaaatcctttg-ttttttataaccaaagtttataaactttcattcttgaaattcaattaactttacaaattcccactatt................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUUACAGAAAAAUUUAAAAUUGAAAUCGUAUAAAAACAAGGGAGGACUGUAUGAAAGACAGAAAUCCUUUGUUUUUUUAUGACUAAAGUUUAUAAACUUUCAUUCUCAAAAUUCAAUUAACUUUACAAAUUCCCACUAUU .....................(((((((.(((((.((((((((((((...((((.......))))...)))))))))))).)))))..((((((....))))))...........)))))))...................... (-28.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAGUGGGAAUUUGUAAAGUUAAUUGAAUUUUGAGAAUGAAAGUUUAUAAACUUUAGUCAUAAAAAAACAAAGGAUUUCUGUCUUUCAUACAGUCCUCCCUUGUUUUUAUACGAUUUCAAUUUUAAAUUUUUCUGUAAAAAAU .((((.(((((((((.......(((((((..(((.((...((((((....))))))..))....((((((((.(((...((((.......))))...))).))))))))...))).))))))).)))))))))))))....... (-26.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 88 41 195 139 smit:SMT_487|5end_transcriptional_regulator,_TetR_family_422380..422610_POSITIVE 226 95 55 178 140 smit:SMT_995|5end_K07574_putative_RNA-binding_protein_containing_KH_domain_936468..936698_NEGATIVE 226 75 41 180 142 smit:SMT_937|5end_dipeptidase_889579..889809_POSITIVE 226 75 41 180 142 smit:SMT_932|5end_tellurite_resistance_protein_885065..885295_POSITIVE 225 74 41 105 65 smit:SMT_127|5end_transcriptional_regulator,_PadR_family_78563..78793_NEGATIVE 222 106 67 71 29 smit:SMT_1575|5end_ribokinase_1568064..1568294_POSITIVE 217 64 37 193 167 smit:SMT_569|5end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_487139..487369_POSITIVE 211 48 24 181 158 smit:SMT_1359|5end_dihydroorotate_dehydrogenase_electron_transfer_subunit_1338003..1338233_NEGATIVE 211 72 41 130 95 smit:SMT_423|5end_sensory_transduction_protein_kinase_366012..366242_POSITIVE 208 69 23 202 164 smit:SMT_517|5end_hypothetical_protein_442896..443126_POSITIVE 207 139 91 149 103 smit:SMT_1328|5end_hypothetical_protein_1304468..1304698_NEGATIVE 201 65 41 66 37 smit:SMT_243|5end_PTS_system,_mannose-specific_IIC_component_180901..181131_NEGATIVE 199 59 24 226 189 smit:SMT_619|5end_riboflavin_kinase_/_FMN_adenylyltransferase_527812..528042_POSITIVE 198 117 71 85 31 smit:SMT_1092|5end_transcription_antitermination_factor_1033696..1033926_NEGATIVE 198 70 23 173 130 smit:SMT_673|5end_K01926_AT-rich_DNA-binding_protein_580902..581132_POSITIVE 198 81 43 112 80 smit:SMT_557|5end_K04488_nitrogen_fixation_protein_NifU_and_related_proteins_474757..474987_POSITIVE 197 82 43 205 168 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 196 90 41 84 17 smit:SMT_357|5end_tRNA_(guanine-N7-)-methyltransferase_293185..293415_POSITIVE 195 88 44 61 13 smit:SMT_1894|5end_K02025_multiple_sugar_transport_system_permease_protein_1846508..1846738_POSITIVE 195 88 44 61 13 smit:SMT_1764|5end_K02025_multiple_sugar_transport_system_permease_protein_1739943..1740173_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 80 31 53 4 smit:SMT_273|3end_glucan_1,6-alpha-glucosidase_215105..215255_POSITIVE 253 80 38 89 50 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 229 106 63 93 45 smit:SMT_1637|3end_hypothetical_protein_1623848..1623998_POSITIVE 226 75 41 52 14 smit:SMT_936|3end_cobyric_acid_synthase_889531..889681_POSITIVE 226 75 41 52 14 smit:SMT_931|3end_cobyric_acid_synthase_885017..885167_POSITIVE 222 106 67 71 29 smit:SMT_1574|3end_K02529_LacI_family_transcriptional_regulator_1568144..1568294_POSITIVE 221 90 43 104 53 smit:SMT_461|3end_mannose-6-phosphate_isomerase_400403..400553_POSITIVE 207 139 91 139 93 smit:SMT_1329|3end_GTP-binding_protein_CgtA_1304478..1304628_NEGATIVE 201 77 42 62 28 smit:SMT_1424|3end_K02003_1410463..1410613_POSITIVE 198 70 23 90 47 smit:SMT_672|3end_hypothetical_protein_580899..581049_POSITIVE 198 81 43 125 93 smit:SMT_556|3end_putative_aminotransferase_474850..475000_POSITIVE 197 73 35 85 51 smit:SMT_162|3end_hypothetical_protein_107134..107284_POSITIVE 196 90 41 87 20 smit:SMT_356|3end_hypothetical_protein_293268..293418_POSITIVE 192 86 43 119 77 smit:SMT_231|3end_translation_elongation_factor_G_168222..168372_POSITIVE 190 79 36 48 7 smit:SMT_636|3end_ribonucleoside-diphosphate_reductase_beta_chain_542195..542345_POSITIVE 188 88 41 136 94 smit:SMT_347|3end_hypothetical_protein_285881..286031_NEGATIVE 186 77 43 55 20 smit:SMT_550|3end_K02945_small_subunit_ribosomal_protein_S1_468942..469092_POSITIVE 185 83 42 65 21 smit:SMT_1334|3end_hypothetical_protein_1308748..1308898_NEGATIVE 185 81 44 116 69 smit:SMT_572|3end_fructose_repressor_491059..491209_POSITIVE 185 68 22 56 8 smit:SMT_427|3end_hypothetical_protein_predicted_by_Glimmer/Critica_369119..369269_POSITIVE