Origin IGS: ttgagaaatttcgtacacaatttctattatttaatgtgtaacagttttacatctctatgcttattggcttgtattgtagtaactacaagtttggcatagggatttttgtttactgaagaggaaaggataagtatgtttcaaggtttgaaatatttttaaactaaacaagagcaaatttttaaaggagatttttcaacgtaacttccacttgtctgaccgaagtggaagttagtctgaaatttatggtggaattaagtatgagacgttagattttttcagaaaattttctaaaacaaacaggatttgtttgacatttatttgaaaattctgtaaaatgaattattatatcgttaaaggagaatatat .........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 atatattctcctttaacgatataataattcattttacagaattttcaaataaatgtcaaacaaatcctgtttgttttagaaaattttctgaaaaaatctaacgtctcatacttaattccaccataaatttcagactaacttccacttcggtcagacaagtggaagttacgttgaaaaatctcctttaaaaatttgctcttgtttagtttaaaaatatttcaaaccttgaaacatacttatcctttcctcttcagtaaacaaaaatccctatgccaaacttgtagttactacaatacaagccaataagcatagagatgtaaaactgttacacattaaataatagaaattgtgtacgaaatttctcaa Mask Tandem Repeat Region ================================================ ttgagaaatttcgtacacaatttctattatttaatgtgtaacagttttacatctctatgcttattggcttgtattgtagtaactacaagtttggcatagggatttttgtttactgaagaggaaaggataagtatgtttcaaggtttgaaatatttttaaactaaacaagagcaaatttttaaaggagatttttcaacgtaacttccacttgtctgaccgaagtggaagttagtctgaaatttatggtggaattaagtatgagacgttagattttttcagaaaattttctaaaacaaacaggatttgtttgacatttatttgaaaattctgtaaaatgaattattatatcgttaaaggagaatatat Find is-nt database================================================ Query_seq: SMT_258:SMT_259|SMT_258:SMT_259:alpha-glucosidase, family 31 of glycosyl hydrolase:dipeptide/tripeptide permease:->->:197403..197768 366 ttgagaaatttcgtacacaatttctattatttaatgtgtaacagttttacatctctatgcttattggcttgtattgtagtaactacaagtttggcatagggatttttgtttactgaagaggaaaggataagtatgtttcaaggtttgaaatatttttaaactaaacaagagcaaatttttaaaggagatttttcaacgtaacttccacttgtctgaccgaagtggaagttagtctgaaatttatggtggaattaagtatgagacgttagattttttcagaaaattttctaaaacaaacaggatttgtttgacatttatttgaaaattctgtaaaatgaattattatatcgttaaaggagaatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_258:SMT_259|SMT_258:SMT_259:alpha-glucosidase, family 31 of glycosyl hydrolase:dipeptide/tripeptide permease:->->:197403..197768 366 ttgagaaatttcgtacacaatttctattatttaatgtgtaacagttttacatctctatgcttattggcttgtattgtagtaactacaagtttggcatagggatttttgtttactgaagaggaaaggataagtatgtttcaaggtttgaaatatttttaaactaaacaagagcaaatttttaaaggagatttttcaacgtaacttccacttgtctgaccgaagtggaagttagtctgaaatttatggtggaattaagtatgagacgttagattttttcagaaaattttctaaaacaaacaggatttgtttgacatttatttgaaaattctgtaaaatgaattattatatcgttaaaggagaatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_258:SMT_259|SMT_258:SMT_259:alpha-glucosidase, family 31 of glycosyl hydrolase:dipeptide/tripeptide permease:->->:197403..197768 366 ttgagaaatttcgtacacaatttctattatttaatgtgtaacagttttacatctctatgcttattggcttgtattgtagtaactacaagtttggcatagggatttttgtttactgaagaggaaaggataagtatgtttcaaggtttgaaatatttttaaactaaacaagagcaaatttttaaaggagatttttcaacgtaacttccacttgtctgaccgaagtggaagttagtctgaaatttatggtggaattaagtatgagacgttagattttttcagaaaattttctaaaacaaacaggatttgtttgacatttatttgaaaattctgtaaaatgaattattatatcgttaaaggagaatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgagaaatttcgtacacaatttctattatttaatgtgtaacagttttacatctctatgcttattggcttgtattgtagtaactacaagtttggcatagggatttttgtttactgaagaggaaaggataagtatgtttcaaggtttgaaatatttttaaactaaacaagagcaaatttttaaaggagatttttcaacgtaacttccacttgtctgaccgaagtggaagttagtctgaaatttatggtggaattaagtatgagacgttagattttttcagaaaattttctaaaacaaacaggatttgtttgacatttatttgaaaattctgtaaaatgaattattatatcgttaaaggagaatatat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 1 End: 96 M R N F V H N F Y Y L M C N S F T S L C L L A C I V V T T S L A .............................................................................................................................................................................................................................................................................. Protein_Len: 32 Strand: - Start: 269 End: 364 ............................................................................................................................................................................................................................................................................ I K E S F K R F C V P N T Q C K N S F E T F H I I I D N F S F M .. Protein_Len: 31 Strand: - Start: 244 End: 336 ................................................................................................................................................................................................................................................... P P I L Y S V N S K K L F N E L V F L I Q K V N I Q F N Q L M .............................. Protein_Len: 42 Strand: - Start: 64 End: 189 ............................................................... Q S T N Y Y S C T Q C L S K Q K S F L F P Y T H K L T Q F I K L S F L L L N K F S M ................................................................................................................................................................................. Protein_Len: 35 Strand: - Start: 30 End: 134 ............................. K I H L L K V D R H K N A Q I T T V V L K A Y P N K N V S S S L I L M ........................................................................................................................................................................................................................................ ttgagaaatttcgtacacaatttctattatttaatgtgtaacagttttacatctctatgcttattggcttgtattgtagtaactacaagtttggcatagggatttttgtttactgaagaggaaaggataagtatgtttcaaggtttgaaatatttttaaactaaacaagagcaaatttttaaaggagatttttcaacgtaacttccacttgtctgaccgaagtggaagttagtctgaaatttatggtggaattaagtatgagacgttagattttttcagaaaattttctaaaacaaacaggatttgtttgacatttatttgaaaattctgtaaaatgaattattatatcgttaaaggagaatatat 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: 91 Start: 307 End: 336 ..................................................................................................................................................................................................................................................................................................................TTTGACATTTATTTGAAAATTCTGTAAAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgagaaatttcgtacacaatttctattatttaatgtgtaacagttttacatctctatgcttattggcttgtattgtagtaactacaagtttggcatagggatttttgtttactgaagaggaaaggataagtatgtttcaaggtttgaaatatttttaaactaaacaagagcaaatttttaaaggagatttttcaacgtaacttccacttgtctgaccgaagtggaagttagtctgaaatttatggtggaattaagtatgagacgttagattttttcagaaaattttctaaaacaaacaggatttgtttgacatttatttgaaaattctgtaaaatgaattattatatcgttaaaggagaatatat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -5.4 Tail_Score: -4.62069 Start: 134 End: 152 Full_Region: AGGAAAGGATAAGTA TGTTTCAA GGT TTGAAATA TTTTTAAACTAAACA .....................................................................................................................................TGTTTCAAGGTTTGAAATA...................................................................................................................................................................................................................... TransTerm Strand: + Conf: 68 HP_score: -6.5 Tail_Score: -3.97834 Start: 191 End: 239 Full_Region: TTTTTAAAGGAGATT TTTCAACGTAACTTCCACTT GTCTGACCG AAGTGGAAGTTAGTCTGAAA TTTATGGTGGAATTA ..............................................................................................................................................................................................TTTCAACGTAACTTCCACTTGTCTGACCGAAGTGGAAGTTAGTCTGAAA............................................................................................................................... TransTerm Strand: - Conf: 65 HP_score: -5.2 Tail_Score: -4.14013 Start: 294 End: 310 Full_Region: ttttcaaataaatgt caaaca aatcc tgtttg ttttagaaaattttc .....................................................................................................................................................................................................................................................................................................caaacaaatcctgtttg........................................................ Find igs database================================================ Query_seq: SMT_258:SMT_259|SMT_258:SMT_259:alpha-glucosidase, family 31 of glycosyl hydrolase:dipeptide/tripeptide permease:->->:197403..197768 366 ttgagaaatttcgtacacaatttctattatttaatgtgtaacagttttacatctctatgcttattggcttgtattgtagtaactacaagtttggcatagggatttttgtttactgaagaggaaaggataagtatgtttcaaggtttgaaatatttttaaactaaacaagagcaaatttttaaaggagatttttcaacgtaacttccacttgtctgaccgaagtggaagttagtctgaaatttatggtggaattaagtatgagacgttagattttttcagaaaattttctaaaacaaacaggatttgtttgacatttatttgaaaattctgtaaaatgaattattatatcgttaaaggagaatatat Intra-Species Hit: Count: 1 Min: 1 Max: 366 Len: 366 Subject: smit_SMT_258_SMT_259|alpha-glucosidase, family 31 of glycosyl hydrolase:dipeptide/tripeptide permease|POSITIVE:POSITIVE|[197403,197768]|366 HSP 1 e-value: 0.0 bit: 726.0 Len: 366 Query Start:1 Query End:366 Subject Strand: POSITIVE Subject Start: 1 Subject End: 366 ttgagaaatttcgtacacaatttctattatttaatgtgtaacagttttacatctctatgcttattggcttgtattgtagtaactacaagtttggcatagggatttttgtttactgaagaggaaaggataagtatgtttcaaggtttgaaatatttttaaactaaacaagagcaaatttttaaaggagatttttcaacgtaacttccacttgtctgaccgaagtggaagttagtctgaaatttatggtggaattaagtatgagacgttagattttttcagaaaattttctaaaacaaacaggatttgtttgacatttatttgaaaattctgtaaaatgaattattatatcgttaaaggagaatatat ttgagaaatttcgtacacaatttctattatttaatgtgtaacagttttacatctctatgcttattggcttgtattgtagtaactacaagtttggcatagggatttttgtttactgaagaggaaaggataagtatgtttcaaggtttgaaatatttttaaactaaacaagagcaaatttttaaaggagatttttcaacgtaacttccacttgtctgaccgaagtggaagttagtctgaaatttatggtggaattaagtatgagacgttagattttttcagaaaattttctaaaacaaacaggatttgtttgacatttatttgaaaattctgtaaaatgaattattatatcgttaaaggagaatatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAGAAAUUUCGUACACAAUUUCUAUUAUUUAAUGUGUAACAGUUUUACAUCUCUAUGCUUAUUGGCUUGUAUUGUAGUAACUACAAGUUUGGCAUAGGGAUUUUUGUUUACUGAAGAGGAAAGGAUAAGUAUGUUUCAAGGUUUGAAAUAUUUUUAAACUAAACAAGAGCAAAUUUUUAAAGGAGAUUUUUCAACGUAACUUCCACUUGUCUGACCGAAGUGGAAGUUAGUCUGAAAUUUAUGGUGGAAUUAAGUAUGAGACGUUAGAUUUUUUCAGAAAAUUUUCUAAAACAAACAGGAUUUGUUUGACAUUUAUUUGAAAAUUCUGUAAAAUGAAUUAUUAUAUCGUUAAAGGAGAAUAUAU ...(((((((........)))))))....((((((((((((.(((((...(((((((((((....((((((((.(......).)))))))).)))))))))))..((((((...(((((.((((((((....((((((((.((((((((.....))))))))........((....(((((....(((((((...((.((((((((((((.........))))))))))))))..)))))))....)))))....)).))))))))...))))))))......)))))..))))))(((((((((.................))))))))).....))))).))))).)))))))........... (-83.73) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAUUCUCCUUUAACGAUAUAAUAAUUCAUUUUACAGAAUUUUCAAAUAAAUGUCAAACAAAUCCUGUUUGUUUUAGAAAAUUUUCUGAAAAAAUCUAACGUCUCAUACUUAAUUCCACCAUAAAUUUCAGACUAACUUCCACUUCGGUCAGACAAGUGGAAGUUACGUUGAAAAAUCUCCUUUAAAAAUUUGCUCUUGUUUAGUUUAAAAAUAUUUCAAACCUUGAAACAUACUUAUCCUUUCCUCUUCAGUAAACAAAAAUCCCUAUGCCAAACUUGUAGUUACUACAAUACAAGCCAAUAAGCAUAGAGAUGUAAAACUGUUACACAUUAAAUAAUAGAAAUUGUGUACGAAAUUUCUCAA ................(((((((((......(((((.(((((((((...((((...((((((.....)))))).))))))))))))).))))).......(((((((((.((((.......((((..((((((..((((((((((((.(......)))))))))))))..))))))...............((((((...(...((..(((..((.(((((.....))))).))..)))..)).....)...))))))..........)))).....((((((..........))))))....)))).)).)))))))....((((((.........))))))..))))))).))........... (-61.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 230 183 133 76 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 301 89 41 78 33 smit:SMT_608|5end_laminin-binding_surface_protein_520757..520987_POSITIVE 277 228 196 204 172 smit:SMT_903|5end_hypothetical_protein_852310..852540_NEGATIVE 263 227 183 194 142 smit:SMT_726|5end_ImpB/MucB/SamB_family_protein_631827..632057_NEGATIVE 261 245 203 56 15 smit:SMT_1425|5end_hypothetical_protein_1410805..1411035_NEGATIVE 261 250 202 74 25 smit:SMT_657|5end_Kef-type_K+_transport_system,_predicted_NAD-binding_component_569104..569334_NEGATIVE 257 249 201 150 98 smit:SMT_2059|5end_hypothetical_protein_1967881..1968111_POSITIVE 252 97 54 73 11 smit:SMT_1822|5end_hypothetical_protein_1794452..1794682_POSITIVE 252 139 91 94 33 smit:SMT_1008|5end_hypothetical_protein_948021..948251_NEGATIVE 248 95 51 182 120 smit:SMT_557|5end_K04488_nitrogen_fixation_protein_NifU_and_related_proteins_474757..474987_POSITIVE 248 109 64 160 109 smit:SMT_145|5end_hypothetical_protein_95873..96103_POSITIVE 247 229 188 133 98 smit:SMT_723|5end_hypothetical_protein_629475..629705_NEGATIVE 244 100 52 162 108 smit:SMT_1134|5end_glutamyl-tRNA_synthetase_1076464..1076694_NEGATIVE 242 235 203 72 40 smit:SMT_359|5end_transcription_termination-antitermination_factor_294470..294700_POSITIVE 241 250 202 196 152 smit:SMT_848|5end_hypothetical_protein_795153..795383_NEGATIVE 240 217 171 174 130 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 238 56 13 171 126 smit:SMT_1299|5end_MutT/NUDIX_family_protein_1261719..1261949_POSITIVE 237 100 51 76 27 smit:SMT_1703|5end_recombination_protein_RecR_1686660..1686890_POSITIVE 237 136 92 164 122 smit:SMT_715|5end_DHH_subfamily_1_protein_621379..621609_POSITIVE 234 280 232 215 159 smit:SMT_1037|5end_alpha-galactosidase_979609..979839_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 230 183 118 61 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 301 89 41 57 12 smit:SMT_607|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520816..520966_POSITIVE 255 269 222 132 83 smit:SMT_1681|3end_D-alanine-activating_enzyme_1665052..1665202_POSITIVE 250 228 183 151 95 smit:SMT_347|3end_hypothetical_protein_285881..286031_NEGATIVE 248 109 64 55 4 smit:SMT_144|3end_hypothetical_protein_predicted_by_Glimmer/Critica_95848..95998_POSITIVE 241 148 102 151 111 smit:SMT_387|3end_hypothetical_protein_predicted_by_Glimmer/Critica_321118..321268_POSITIVE 237 100 51 65 16 smit:SMT_1702|3end_penicillin-binding_protein_2B_1686729..1686879_POSITIVE 237 119 83 95 55 smit:SMT_1654|3end_K03110_signal_recognition_particle_receptor_1643519..1643669_POSITIVE 235 95 57 129 94 smit:SMT_1465|3end_hypothetical_protein_1446745..1446895_POSITIVE 232 236 211 129 99 smit:SMT_1891|3end_putative_dihydrolipoamide_S-acetyltransferase_1845019..1845169_POSITIVE 232 116 83 97 60 smit:SMT_1591|3end_DNA-entry_nuclease_1579468..1579618_POSITIVE 232 217 185 148 122 smit:SMT_237|3end_aminopeptidase_C_176493..176643_POSITIVE 231 72 33 67 16 smit:SMT_1225|3end_50S_ribosomal_protein_L13_1188798..1188948_POSITIVE 231 229 187 61 23 smit:SMT_866|3end_50S_ribosomal_protein_L11_815809..815959_NEGATIVE 229 227 183 74 25 smit:SMT_1920|3end_ABC_transporter,_ATP-binding_protein_1862736..1862886_NEGATIVE 228 222 190 151 116 smit:SMT_930|3end_ATP-dependent_RNA_helicase_883389..883539_NEGATIVE 227 89 50 57 18 smit:SMT_1730|3end_geranyltranstransferase_1715730..1715880_POSITIVE 224 210 170 41 4 smit:SMT_1409|3end_hypothetical_protein_1387336..1387486_NEGATIVE 223 107 66 91 54 smit:SMT_753|3end_chorismate_synthase_656801..656951_NEGATIVE 220 95 54 129 91 smit:SMT_2059|3end_hypothetical_protein_1968710..1968860_POSITIVE