Origin IGS: cagctgaggaaaaaacagcagctaaagaagaagcgaaagccaaagcagacgcagcgaagactgcaatcgacaatgcgacaacaaataatgcagtaactcaagctaaaaacgctggagcaacgagtgtatcttcagtaaatccaacagcgcaagctaagccagcagctaagaaagcaatagacgatgcgcttaaagctaagaacgatgcaatcgat .........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 atcgattgcatcgttcttagctttaagcgcatcgtctattgctttcttagctgctggcttagcttgcgctgttggatttactgaagatacactcgttgctccagcgtttttagcttgagttactgcattatttgttgtcgcattgtcgattgcagtcttcgctgcgtctgctttggctttcgcttcttctttagctgctgttttttcctcagctg Mask Tandem Repeat Region ================================================ cagctgaggaaaaaacagcagctaaagaagaagcgaaagccaaagcagacgcagcgaagactgcaatcgacaatgcgacaacaaataatgcagtaactcaagctaaaaacgctggagcaacgagtgtatcttcagtaaatccaacagcgcaagctaagccagcagctaagaaagcaatagacgatgcgcttaaagctaagaacgatgcaatcgat Find is-nt database================================================ Query_seq: SMT_1939:SMT_1940|SMT_1939:SMT_1940:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:->->:1876514..1876728 215 cagctgaggaaaaaacagcagctaaagaagaagcgaaagccaaagcagacgcagcgaagactgcaatcgacaatgcgacaacaaataatgcagtaactcaagctaaaaacgctggagcaacgagtgtatcttcagtaaatccaacagcgcaagctaagccagcagctaagaaagcaatagacgatgcgcttaaagctaagaacgatgcaatcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1939:SMT_1940|SMT_1939:SMT_1940:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:->->:1876514..1876728 215 cagctgaggaaaaaacagcagctaaagaagaagcgaaagccaaagcagacgcagcgaagactgcaatcgacaatgcgacaacaaataatgcagtaactcaagctaaaaacgctggagcaacgagtgtatcttcagtaaatccaacagcgcaagctaagccagcagctaagaaagcaatagacgatgcgcttaaagctaagaacgatgcaatcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1939:SMT_1940|SMT_1939:SMT_1940:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:->->:1876514..1876728 215 cagctgaggaaaaaacagcagctaaagaagaagcgaaagccaaagcagacgcagcgaagactgcaatcgacaatgcgacaacaaataatgcagtaactcaagctaaaaacgctggagcaacgagtgtatcttcagtaaatccaacagcgcaagctaagccagcagctaagaaagcaatagacgatgcgcttaaagctaagaacgatgcaatcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagctgaggaaaaaacagcagctaaagaagaagcgaaagccaaagcagacgcagcgaagactgcaatcgacaatgcgacaacaaataatgcagtaactcaagctaaaaacgctggagcaacgagtgtatcttcagtaaatccaacagcgcaagctaagccagcagctaagaaagcaatagacgatgcgcttaaagctaagaacgatgcaatcgat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 4 End: 93 ... M R K K Q Q L K K K R K P K Q T Q R R L Q S T M R Q Q I M Q .......................................................................................................................... Protein_Len: 50 Strand: + Start: 66 End: 215 ................................................................. M D N A T T N N A V T Q A K N A G A T S V S S V N P T A Q A K P A A K K A I D D A L K A K N D A I D Protein_Len: 37 Strand: - Start: 101 End: 211 .................................................................................................... A L F A P A V L T D E T F G V A C A L G A A L F A I S S A S L A L F S A M .... Protein_Len: 33 Strand: - Start: 3 End: 101 .. S L F F C C S F F F R F G F C V C R L S C D V I R C C I I C Y S M .................................................................................................................. cagctgaggaaaaaacagcagctaaagaagaagcgaaagccaaagcagacgcagcgaagactgcaatcgacaatgcgacaacaaataatgcagtaactcaagctaaaaacgctggagcaacgagtgtatcttcagtaaatccaacagcgcaagctaagccagcagctaagaaagcaatagacgatgcgcttaaagctaagaacgatgcaatcgat 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================================================ cagctgaggaaaaaacagcagctaaagaagaagcgaaagccaaagcagacgcagcgaagactgcaatcgacaatgcgacaacaaataatgcagtaactcaagctaaaaacgctggagcaacgagtgtatcttcagtaaatccaacagcgcaagctaagccagcagctaagaaagcaatagacgatgcgcttaaagctaagaacgatgcaatcgat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 78 HP_score: -5.5 Tail_Score: -4.75776 Start: 110 End: 122 Full_Region: tactgaagatacact cgttg ctc cagcg tttttagcttgagtt .............................................................................................................cgttgctccagcg............................................................................................. Find igs database================================================ Query_seq: SMT_1939:SMT_1940|SMT_1939:SMT_1940:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:->->:1876514..1876728 215 cagctgaggaaaaaacagcagctaaagaagaagcgaaagccaaagcagacgcagcgaagactgcaatcgacaatgcgacaacaaataatgcagtaactcaagctaaaaacgctggagcaacgagtgtatcttcagtaaatccaacagcgcaagctaagccagcagctaagaaagcaatagacgatgcgcttaaagctaagaacgatgcaatcgat Intra-Species Hit: Count: 1 Min: 1 Max: 215 Len: 215 Subject: smit_SMT_1939_SMT_1940|hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[1876514,1876728]|215 HSP 1 e-value: 1.0E-118 bit: 426.0 Len: 215 Query Start:1 Query End:215 Subject Strand: POSITIVE Subject Start: 1 Subject End: 215 cagctgaggaaaaaacagcagctaaagaagaagcgaaagccaaagcagacgcagcgaagactgcaatcgacaatgcgacaacaaataatgcagtaactcaagctaaaaacgctggagcaacgagtgtatcttcagtaaatccaacagcgcaagctaagccagcagctaagaaagcaatagacgatgcgcttaaagctaagaacgatgcaatcgat cagctgaggaaaaaacagcagctaaagaagaagcgaaagccaaagcagacgcagcgaagactgcaatcgacaatgcgacaacaaataatgcagtaactcaagctaaaaacgctggagcaacgagtgtatcttcagtaaatccaacagcgcaagctaagccagcagctaagaaagcaatagacgatgcgcttaaagctaagaacgatgcaatcgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGCUGAGGAAAAAACAGCAGCUAAAGAAGAAGCGAAAGCCAAAGCAGACGCAGCGAAGACUGCAAUCGACAAUGCGACAACAAAUAAUGCAGUAACUCAAGCUAAAAACGCUGGAGCAACGAGUGUAUCUUCAGUAAAUCCAACAGCGCAAGCUAAGCCAGCAGCUAAGAAAGCAAUAGACGAUGCGCUUAAAGCUAAGAACGAUGCAAUCGAU .(((((..(......)..))))).........((....))....(((...((((......))))..(((......)))..........))).....(((.(((.......))).)))...(((.(((((((((............(((....)))........(((((((...(((........))).)))..))))..))).)))))).))).. (-50.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGAUUGCAUCGUUCUUAGCUUUAAGCGCAUCGUCUAUUGCUUUCUUAGCUGCUGGCUUAGCUUGCGCUGUUGGAUUUACUGAAGAUACACUCGUUGCUCCAGCGUUUUUAGCUUGAGUUACUGCAUUAUUUGUUGUCGCAUUGUCGAUUGCAGUCUUCGCUGCGUCUGCUUUGGCUUUCGCUUCUUCUUUAGCUGCUGUUUUUUCCUCAGCUG ...((((((((((.....((((..((((((.................((((.((.(((...))).))))))..(((...((.((........))))...))).))))))..))))...((.((.(((.....))).)).)).....))).)))))))......(((...((....))...)))........((((((..(......)..)))))) (-50.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 80 37 81 42 smit:SMT_927|5end_KH_domain_protein_882677..882907_NEGATIVE 365 190 148 55 19 smit:SMT_147|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_97406..97636_POSITIVE 365 190 148 55 19 smit:SMT_119|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_70457..70687_POSITIVE 338 60 17 71 26 smit:SMT_274|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_215221..215451_POSITIVE 325 188 148 63 22 smit:SMT_1293|5end_K02051_sulfonate/nitrate/taurine_transport_system_substrate-binding_protein_1254976..1255206_POSITIVE 314 189 148 61 22 smit:SMT_1260|5end_hypothetical_protein_1225517..1225747_POSITIVE 308 78 33 96 42 smit:SMT_1923|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1866021..1866251_POSITIVE 308 150 101 69 20 smit:SMT_1142|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1085546..1085776_POSITIVE 303 167 133 208 164 smit:SMT_1739|5end_hypothetical_protein_1721263..1721493_POSITIVE 303 190 141 83 31 smit:SMT_518|5end_biotin_synthase_443751..443981_NEGATIVE 302 69 22 172 120 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 298 168 121 77 21 smit:SMT_793|5end_K02029_polar_amino_acid_transport_system_permease_protein_703236..703466_NEGATIVE 297 170 125 213 166 smit:SMT_1386|5end_phosphoenolpyruvate-protein_phosphotransferase_1362806..1363036_POSITIVE 291 77 31 94 37 smit:SMT_1775|5end_K07478_putative_ATPase_1751836..1752066_NEGATIVE 291 159 111 182 140 smit:SMT_1359|5end_dihydroorotate_dehydrogenase_electron_transfer_subunit_1338003..1338233_NEGATIVE 291 165 121 69 16 smit:SMT_243|5end_PTS_system,_mannose-specific_IIC_component_180901..181131_NEGATIVE 287 189 141 210 153 smit:SMT_1972|5end_uncharacterized_conserved_phage_related_protein_1903662..1903892_POSITIVE 287 189 141 225 168 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 287 165 121 215 167 smit:SMT_903|5end_hypothetical_protein_852310..852540_NEGATIVE 287 160 111 222 157 smit:SMT_568|5end_hypothetical_protein_485674..485904_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 526 106 61 48 3 smit:SMT_2092|3end_malolactic_enzyme_1987040..1987190_NEGATIVE 442 197 152 77 35 smit:SMT_2057|3end_cell_division_protein_FtsH_1966897..1967047_NEGATIVE 314 189 148 42 3 smit:SMT_1259|3end_hypothetical_protein_1225578..1225728_POSITIVE 298 168 121 68 12 smit:SMT_794|3end_hypothetical_protein_703245..703395_NEGATIVE 292 62 22 147 105 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 287 73 33 64 14 smit:SMT_1776|3end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_1751892..1752042_NEGATIVE 287 46 2 78 23 smit:SMT_1524|3end_peptidase_T_1505867..1506017_POSITIVE 283 55 16 56 14 smit:SMT_1865|3end_D-alanyl_carrier_protein_1827377..1827527_POSITIVE 283 55 16 56 14 smit:SMT_1312|3end_D-alanyl_carrier_protein_1277361..1277511_POSITIVE 279 189 148 60 14 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 275 133 92 74 31 smit:SMT_234|3end_aminopeptidase_PepS_174151..174301_POSITIVE 274 170 146 50 29 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 273 209 164 51 3 smit:SMT_1489|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1470714..1470864_POSITIVE 269 210 162 138 97 smit:SMT_1950|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_1885069..1885219_POSITIVE 268 68 21 92 45 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 268 167 125 146 115 smit:SMT_1284|3end_predicted_amidophosphoribosyltransferase_1247704..1247854_POSITIVE 268 168 132 56 8 smit:SMT_951|3end_oxidoreductase,_DadA_family_protein/D-amino_acid_oxidase_898995..899145_NEGATIVE 265 180 140 48 4 smit:SMT_480|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416765..416915_NEGATIVE 264 77 32 60 12 smit:SMT_1956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1889537..1889687_NEGATIVE 264 77 32 55 7 smit:SMT_387|3end_hypothetical_protein_predicted_by_Glimmer/Critica_321118..321268_POSITIVE