Origin IGS: aaaggtttctaaagcattatcttatccatacaccttcccttccagcnnnnnttaattaattaannnnnagttgtgtctaacactcatcaatcctaatgcccactacgaccctatcccagtcaagaagccagagacaatctccagaagaatcaatgatccaggaatcattgcagcttgccactgtggagatgagtacgaaactgaatattcagaatcgatcgagactcacacagcaacatcgatcgacagcggtaaccagaaatcgactgacataccacatgacaaatcggtcgatagtaatccagatgagttggagaatgattactacaaccccactttgacgcttacacmagacaatat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 atattgtctkgtgtaagcgtcaaagtggggttgtagtaatcattctccaactcatctggattactatcgaccgatttgtcatgtggtatgtcagtcgatttctggttaccgctgtcgatcgatgttgctgtgtgagtctcgatcgattctgaatattcagtttcgtactcatctccacagtggcaagctgcaatgattcctggatcattgattcttctggagattgtctctggcttcttgactgggatagggtcgtagtgggcattaggattgatgagtgttagacacaactnnnnnttaattaattaannnnngctggaagggaaggtgtatggataagataatgctttagaaaccttt Mask Tandem Repeat Region ================================================ aaaggtttctaaagcattatcttatccatacaccttcccttccagcnnnnnttaattaattaannnnnagttgtgtctaacactcatcaatcctaatgcccactacgaccctatcccagtcaagaagccagagacaatctccagaagaatcaatgatccaggaatcattgcagcttgccactgtggagatgagtacgaaactgaatattcagaatcgatcgagactcacacagcaacatcgatcgacagcggtaaccagaaatcgactgacataccacatgacaaatcggtcgatagtaatccagatgagttggagaatgattactacaaccccactttgacgcttacacmagacaatat Find is-nt database================================================ Query_seq: SMT_1853:SMT_1854|SMT_1853:SMT_1854:1,4-alpha-glucan branching enzyme:hypothetical protein predicted by Glimmer/Critica:<-->:1818155..1818514 360 aaaggtttctaaagcattatcttatccatacaccttcccttccagcnnnnnttaattaattaannnnnagttgtgtctaacactcatcaatcctaatgcccactacgaccctatcccagtcaagaagccagagacaatctccagaagaatcaatgatccaggaatcattgcagcttgccactgtggagatgagtacgaaactgaatattcagaatcgatcgagactcacacagcaacatcgatcgacagcggtaaccagaaatcgactgacataccacatgacaaatcggtcgatagtaatccagatgagttggagaatgattactacaaccccactttgacgcttacacmagacaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1853:SMT_1854|SMT_1853:SMT_1854:1,4-alpha-glucan branching enzyme:hypothetical protein predicted by Glimmer/Critica:<-->:1818155..1818514 360 aaaggtttctaaagcattatcttatccatacaccttcccttccagcnnnnnttaattaattaannnnnagttgtgtctaacactcatcaatcctaatgcccactacgaccctatcccagtcaagaagccagagacaatctccagaagaatcaatgatccaggaatcattgcagcttgccactgtggagatgagtacgaaactgaatattcagaatcgatcgagactcacacagcaacatcgatcgacagcggtaaccagaaatcgactgacataccacatgacaaatcggtcgatagtaatccagatgagttggagaatgattactacaaccccactttgacgcttacacmagacaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1853:SMT_1854|SMT_1853:SMT_1854:1,4-alpha-glucan branching enzyme:hypothetical protein predicted by Glimmer/Critica:<-->:1818155..1818514 360 aaaggtttctaaagcattatcttatccatacaccttcccttccagcnnnnnttaattaattaannnnnagttgtgtctaacactcatcaatcctaatgcccactacgaccctatcccagtcaagaagccagagacaatctccagaagaatcaatgatccaggaatcattgcagcttgccactgtggagatgagtacgaaactgaatattcagaatcgatcgagactcacacagcaacatcgatcgacagcggtaaccagaaatcgactgacataccacatgacaaatcggtcgatagtaatccagatgagttggagaatgattactacaaccccactttgacgcttacacmagacaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaggtttctaaagcattatcttatccatacaccttcccttccagcnnnnnttaattaattaannnnnagttgtgtctaacactcatcaatcctaatgcccactacgaccctatcccagtcaagaagccagagacaatctccagaagaatcaatgatccaggaatcattgcagcttgccactgtggagatgagtacgaaactgaatattcagaatcgatcgagactcacacagcaacatcgatcgacagcggtaaccagaaatcgactgacataccacatgacaaatcggtcgatagtaatccagatgagttggagaatgattactacaaccccactttgacgcttacacmagacaatat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 90 End: 338 ......................................................................................... M L M P T T T L S Q S R S Q R Q S P E E S M I Q E S L Q L A T V E M S T K L N I Q N R S R L T Q Q H R S T A V T R N R L ...................... Protein_Len: 60 Strand: + Start: 59 End: 358 .......................................................... M X X X L C L T L I N P N A H Y D P I P V K K P E T I S R R I N D P G I I A A C H C G D E Y E T E Y S E S I E T H T A T .. Protein_Len: 49 Strand: - Start: 212 End: 358 ................................................................................................................................................................................................................... F R D L S V C C C R D V A T V L F R S V Y W M V F R D I T I W I L Q L I I V V V G S Q R K C X V M .. Protein_Len: 46 Strand: - Start: 168 End: 305 ....................................................................................................................................................................... Q L K G S H L H T R F Q I N L I S R S E C L L M S R C R Y G S I S Q C V V H C I P R Y Y D M ....................................................... Protein_Len: 38 Strand: - Start: 106 End: 219 ......................................................................................................... S G I G T L F G S V I E L L I L S G P I M A A Q W Q P S S Y S V S Y E S D M ............................................................................................................................................. Protein_Len: 43 Strand: - Start: 80 End: 208 ............................................................................... C E D I R I G V V V R D W D L L W L C D G S S D I I W S D N C S A V T S I L V F S F M ........................................................................................................................................................ aaaggtttctaaagcattatcttatccatacaccttcccttccagcnnnnnttaattaattaannnnnagttgtgtctaacactcatcaatcctaatgcccactacgaccctatcccagtcaagaagccagagacaatctccagaagaatcaatgatccaggaatcattgcagcttgccactgtggagatgagtacgaaactgaatattcagaatcgatcgagactcacacagcaacatcgatcgacagcggtaaccagaaatcgactgacataccacatgacaaatcggtcgatagtaatccagatgagttggagaatgattactacaaccccactttgacgcttacacmagacaatat 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================================================ aaaggtttctaaagcattatcttatccatacaccttcccttccagcnnnnnttaattaattaannnnnagttgtgtctaacactcatcaatcctaatgcccactacgaccctatcccagtcaagaagccagagacaatctccagaagaatcaatgatccaggaatcattgcagcttgccactgtggagatgagtacgaaactgaatattcagaatcgatcgagactcacacagcaacatcgatcgacagcggtaaccagaaatcgactgacataccacatgacaaatcggtcgatagtaatccagatgagttggagaatgattactacaaccccactttgacgcttacacmagacaatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1853:SMT_1854|SMT_1853:SMT_1854:1,4-alpha-glucan branching enzyme:hypothetical protein predicted by Glimmer/Critica:<-->:1818155..1818514 360 aaaggtttctaaagcattatcttatccatacaccttcccttccagcnnnnnttaattaattaannnnnagttgtgtctaacactcatcaatcctaatgcccactacgaccctatcccagtcaagaagccagagacaatctccagaagaatcaatgatccaggaatcattgcagcttgccactgtggagatgagtacgaaactgaatattcagaatcgatcgagactcacacagcaacatcgatcgacagcggtaaccagaaatcgactgacataccacatgacaaatcggtcgatagtaatccagatgagttggagaatgattactacaaccccactttgacgcttacacmagacaatat Intra-Species Hit: Count: 1 Min: 1 Max: 360 Len: 360 Subject: smit_SMT_1853_SMT_1854|1,4-alpha-glucan branching enzyme:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:POSITIVE|[1818155,1818514]|360 HSP 1 e-value: 0.0 bit: 651.0 Len: 360 Query Start:1 Query End:360 Subject Strand: POSITIVE Subject Start: 1 Subject End: 360 aaaggtttctaaagcattatcttatccatacaccttcccttccagcnnnnnttaattaattaannnnnagttgtgtctaacactcatcaatcctaatgcccactacgaccctatcccagtcaagaagccagagacaatctccagaagaatcaatgatccaggaatcattgcagcttgccactgtggagatgagtacgaaactgaatattcagaatcgatcgagactcacacagcaacatcgatcgacagcggtaaccagaaatcgactgacataccacatgacaaatcggtcgatagtaatccagatgagttggagaatgattactacaaccccactttgacgcttacacmagacaatat aaaggtttctaaagcattatcttatccatacaccttcccttccagcnnnnnttaattaattaannnnnagttgtgtctaacactcatcaatcctaatgcccactacgaccctatcccagtcaagaagccagagacaatctccagaagaatcaatgatccaggaatcattgcagcttgccactgtggagatgagtacgaaactgaatattcagaatcgatcgagactcacacagcaacatcgatcgacagcggtaaccagaaatcgactgacataccacatgacaaatcggtcgatagtaatccagatgagttggagaatgattactacaaccccactttgacgcttacacmagacaatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGGUUUCUAAAGCAUUAUCUUAUCCAUACACCUUCCCUUCCAGCNNNNNUUAAUUAAUUAANNNNNAGUUGUGUCUAACACUCAUCAAUCCUAAUGCCCACUACGACCCUAUCCCAGUCAAGAAGCCAGAGACAAUCUCCAGAAGAAUCAAUGAUCCAGGAAUCAUUGCAGCUUGCCACUGUGGAGAUGAGUACGAAACUGAAUAUUCAGAAUCGAUCGAGACUCACACAGCAACAUCGAUCGACAGCGGUAACCAGAAAUCGACUGACAUACCACAUGACAAAUCGGUCGAUAGUAAUCCAGAUGAGUUGGAGAAUGAUUACUACAACCCCACUUUGACGCUUACACMAGACAAUAU ....((((...((((...(((...((((..............((((.....((((....))))......))))........(((((((........(((((....((((.(..(((((((....((((..(((.....))).........(((((((......)))))))..))))...)))).)))...).)).))...((((....))))..((((((((................))))))))..).)))).......((((((((((((.....))).....))))))))).........)))))))))))....))).....(((.......)))..)))).....))))..... (-67.19) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUGUCUKGUGUAAGCGUCAAAGUGGGGUUGUAGUAAUCAUUCUCCAACUCAUCUGGAUUACUAUCGACCGAUUUGUCAUGUGGUAUGUCAGUCGAUUUCUGGUUACCGCUGUCGAUCGAUGUUGCUGUGUGAGUCUCGAUCGAUUCUGAAUAUUCAGUUUCGUACUCAUCUCCACAGUGGCAAGCUGCAAUGAUUCCUGGAUCAUUGAUUCUUCUGGAGAUUGUCUCUGGCUUCUUGACUGGGAUAGGGUCGUAGUGGGCAUUAGGAUUGAUGAGUGUUAGACACAACUNNNNNUUAAUUAAUUAANNNNNGCUGGAAGGGAAGGUGUAUGGAUAAGAUAAUGCUUUAGAAACCUUU .((((((((..(.((.((..(....(((((.((.......))..))))).(((.((..(......((((((.(((.(..(....)..).))).))))))(((((((..((((((.(((((..(((..(((((.(((.......(((..((((....))))..))).......))))))))..)))............(((..(.(((..((.....(..(((.....)))..)..)).))))..)))...)))))))))))..))))))).......(((.....)))...........................)..)).)))..)..)).)).)..)))))))).............. (-98.54) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1003 140 91 231 182 smit:SMT_1853|5end_1,4-alpha-glucan_branching_enzyme_1818064..1818294_NEGATIVE 361 266 221 102 51 smit:SMT_1797|5end_threonine_dehydratase_1772684..1772914_NEGATIVE 349 136 92 124 81 smit:SMT_2045|5end_K+_transport_system,_NAD-binding_component_1956139..1956369_POSITIVE 309 148 102 136 81 smit:SMT_1993|5end_hypothetical_protein_1919800..1920030_NEGATIVE 304 313 271 73 28 smit:SMT_1933|5end_K02006_cobalt_transport_system_ATP-binding_protein_1872222..1872452_NEGATIVE 304 148 101 223 172 smit:SMT_1626|5end_undecaprenyl-diphosphatase_1616028..1616258_NEGATIVE 303 260 216 174 132 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 303 278 238 179 132 smit:SMT_1426|5end_K03095_SprT-like_protein_1411313..1411543_NEGATIVE 303 277 231 77 37 smit:SMT_1382|5end_glutamate_5-kinase_1360744..1360974_NEGATIVE 297 190 141 130 60 smit:SMT_1835|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1803894..1804124_POSITIVE 297 184 141 220 178 smit:SMT_1637|5end_hypothetical_protein_1623091..1623321_POSITIVE 294 259 216 99 57 smit:SMT_1775|5end_K07478_putative_ATPase_1751836..1752066_NEGATIVE 294 273 231 91 46 smit:SMT_243|5end_PTS_system,_mannose-specific_IIC_component_180901..181131_NEGATIVE 288 191 152 225 186 smit:SMT_1107|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1048081..1048311_NEGATIVE 285 160 111 148 96 smit:SMT_1393|5end_hypothetical_protein_1369106..1369336_POSITIVE 285 310 261 199 150 smit:SMT_1366|5end_K02238_competence_protein_ComEC_1346888..1347118_NEGATIVE 282 280 231 91 34 smit:SMT_2016|5end_tyrosine_recombinase_1933425..1933655_NEGATIVE 282 279 235 101 44 smit:SMT_1837|5end_adenylosuccinate_synthetase_1805033..1805263_NEGATIVE 282 130 100 201 166 smit:SMT_929|5end_hypothetical_protein_883342..883572_NEGATIVE 280 142 108 44 2 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 284 241 66 5 smit:SMT_198|3end_50S_ribosomal_protein_L17_129281..129431_POSITIVE 300 270 227 147 108 smit:SMT_862|3end_hypothetical_protein_predicted_by_Glimmer/Critica_809191..809341_POSITIVE 294 259 216 43 1 smit:SMT_1776|3end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_1751892..1752042_NEGATIVE 287 130 83 71 19 smit:SMT_239|3end_hypothetical_protein_177788..177938_POSITIVE 285 160 111 148 96 smit:SMT_1392|3end_dihydroxyacetone_kinase_1369186..1369336_POSITIVE 282 279 235 72 15 smit:SMT_1838|3end_response_regulator_1805062..1805212_NEGATIVE 279 289 241 77 25 smit:SMT_2040|3end_transcription-repair_coupling_factor_1950463..1950613_NEGATIVE 277 277 234 55 1 smit:SMT_1606|3end_glutamate_racemase_1596731..1596881_POSITIVE 277 149 101 81 29 smit:SMT_681|3end_choline_kinase_589952..590102_NEGATIVE 274 130 85 77 22 smit:SMT_1607|3end_K03341_putative_deoxyribonucleotide_triphosphate_pyrophosphatase_1597699..1597849_POSITIVE 274 132 97 46 17 smit:SMT_219|3end_phosphatidate_cytidylyltransferase_151805..151955_POSITIVE 272 260 215 39 5 smit:SMT_1397|3end_mutator_MutT_protein_1373271..1373421_POSITIVE 271 131 91 149 117 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 270 254 214 84 39 smit:SMT_1667|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1657439..1657589_NEGATIVE 269 189 142 59 8 smit:SMT_464|3end_ribonuclease_Z_403303..403453_POSITIVE 269 189 142 59 8 smit:SMT_416|3end_ribonuclease_Z_360432..360582_POSITIVE 266 144 103 62 11 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 264 186 141 46 2 smit:SMT_2067|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1974216..1974366_POSITIVE 260 254 212 55 20 smit:SMT_1315|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1280952..1281102_POSITIVE 259 186 143 77 37 smit:SMT_418|3end_putative_transcriptional_regulator_361232..361382_NEGATIVE