Origin IGS: acacgtccagtggacgtgtttagcactgcgctagaaattagaaacgcaggcacatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagttatgagactttattgaggcagttgattgaacctgtaattaaggagatgtat .........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 atacatctccttaattacaggttcaatcaactgcctcaataaagtctcataactaacaaaaacgaggccaggattttcgtcccgacctcttacctggttagctaataactagctactatgaatattagcttggggtaaaacatccactggatgtgcctgcgtttctaatttctagcgcagtgctaaacacgtccactggacgtgt Mask Tandem Repeat Region ================================================ acacgtccagtggacgtgtttagcactgcgctagaaattagaaacgcaggcacatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagttatgagactttattgaggcagttgattgaacctgtaattaaggagatgtat Find is-nt database================================================ Query_seq: SMT_159:SMT_160|SMT_159:SMT_160:hypothetical protein:folylpolyglutamate synthase:->->:104676..104880 205 acacgtccagtggacgtgtttagcactgcgctagaaattagaaacgcaggcacatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagttatgagactttattgaggcagttgattgaacctgtaattaaggagatgtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_159:SMT_160|SMT_159:SMT_160:hypothetical protein:folylpolyglutamate synthase:->->:104676..104880 205 acacgtccagtggacgtgtttagcactgcgctagaaattagaaacgcaggcacatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagttatgagactttattgaggcagttgattgaacctgtaattaaggagatgtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_159:SMT_160|SMT_159:SMT_160:hypothetical protein:folylpolyglutamate synthase:->->:104676..104880 205 acacgtccagtggacgtgtttagcactgcgctagaaattagaaacgcaggcacatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagttatgagactttattgaggcagttgattgaacctgtaattaaggagatgtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acacgtccagtggacgtgtttagcactgcgctagaaattagaaacgcaggcacatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagttatgagactttattgaggcagttgattgaacctgtaattaaggagatgtat Predict ORF larger than 30AA ================================================ acacgtccagtggacgtgtttagcactgcgctagaaattagaaacgcaggcacatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagttatgagactttattgaggcagttgattgaacctgtaattaaggagatgtat 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================================================ acacgtccagtggacgtgtttagcactgcgctagaaattagaaacgcaggcacatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagttatgagactttattgaggcagttgattgaacctgtaattaaggagatgtat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -7.7 Tail_Score: -4.07885 Start: 53 End: 65 Full_Region: TTAGAAACGCAGGCA CATCC AGT GGATG TTTTACCCCAAGCTA ....................................................CATCCAGTGGATG............................................................................................................................................ TransTerm Strand: + Conf: 83 HP_score: -5.5 Tail_Score: -5.2204 Start: 116 End: 143 Full_Region: TTAGCTAACCAGGTA AGAGGTCGGGA CGAAAA TCCTGGCCTCG TTTTTGTTAGTTATG ...................................................................................................................AGAGGTCGGGACGAAAATCCTGGCCTCG.............................................................. TransTerm Strand: + Conf: 77 HP_score: -9.0 Tail_Score: -3.71597 Start: 117 End: 142 Full_Region: TAGCTAACCAGGTAA GAGGTCGGGA CGAAAA TCCTGGCCTC GTTTTTGTTAGTTAT ....................................................................................................................GAGGTCGGGACGAAAATCCTGGCCTC............................................................... Find igs database================================================ Query_seq: SMT_159:SMT_160|SMT_159:SMT_160:hypothetical protein:folylpolyglutamate synthase:->->:104676..104880 205 acacgtccagtggacgtgtttagcactgcgctagaaattagaaacgcaggcacatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagttatgagactttattgaggcagttgattgaacctgtaattaaggagatgtat Intra-Species Hit: Count: 1 Min: 1 Max: 205 Len: 205 Subject: smit_SMT_159_SMT_160|hypothetical protein:folylpolyglutamate synthase|POSITIVE:POSITIVE|[104676,104880]|205 HSP 1 e-value: 1.0E-112 bit: 406.0 Len: 205 Query Start:1 Query End:205 Subject Strand: POSITIVE Subject Start: 1 Subject End: 205 acacgtccagtggacgtgtttagcactgcgctagaaattagaaacgcaggcacatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagttatgagactttattgaggcagttgattgaacctgtaattaaggagatgtat acacgtccagtggacgtgtttagcactgcgctagaaattagaaacgcaggcacatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagttatgagactttattgaggcagttgattgaacctgtaattaaggagatgtat Inter-species Hit: Count: 2 Min: 12 Max: 154 Len: 143 Subject: NC_008533_SPD_0182_SPD_0183|hypothetical protein:folylpolyglutamate synthase|POSITIVE:POSITIVE|[185363,185812]|450 HSP 1 e-value: 1.0E-32 bit: 141.0 Len: 103 Query Start:52 Query End:154 Subject Strand: POSITIVE Subject Start: 304 Subject End: 406 ...................................................acatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagt................................................... ...................................................acattcagtggatgttttactccacgttaatattcatagttgctagtgattagctaaccaggtaagaggtcgggacgaaaatcctggccttgtttttattagt................................................... HSP 2 e-value: 8.0E-9 bit: 61.9 Len: 39 Query Start:12 Query End:50 Subject Strand: POSITIVE Subject Start: 163 Subject End: 201 ...........ggacgtgtttagcactgcgctagaaattagaaacgcagg........................................................................................................................................................... ...........ggacgtttttagccctgcgctagaaattagaaacgcagg........................................................................................................................................................... Subject: NC_003098_spr0177_spr0178|hypothetical protein:Dihydrofolate:folylpolyglutamate synthetase|POSITIVE:POSITIVE|[185363,185812]|450 HSP 1 e-value: 1.0E-32 bit: 141.0 Len: 103 Query Start:52 Query End:154 Subject Strand: POSITIVE Subject Start: 304 Subject End: 406 ...................................................acatccagtggatgttttaccccaagctaatattcatagtagctagttattagctaaccaggtaagaggtcgggacgaaaatcctggcctcgtttttgttagt................................................... ...................................................acattcagtggatgttttactccacgttaatattcatagttgctagtgattagctaaccaggtaagaggtcgggacgaaaatcctggccttgtttttattagt................................................... HSP 2 e-value: 8.0E-9 bit: 61.9 Len: 39 Query Start:12 Query End:50 Subject Strand: POSITIVE Subject Start: 163 Subject End: 201 ...........ggacgtgtttagcactgcgctagaaattagaaacgcagg........................................................................................................................................................... ...........ggacgtttttagccctgcgctagaaattagaaacgcagg........................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGACGUGUUUAGCACUGCGCUAGAAAUUAGAAACGCAGGCACAUCCAGUGGAUGUUUUACCCCAAGCUAAUAUUCAUAGUAGCUAGUUAUUAGCUAACCAGGUAAGAGGUCGGGACGAAAAUCCUGGCCUCGUUUUUGUUAGU ((.........((.(((((((((...))))...))))))).(((((...))))).......))..(((((((.......(((((((...))))))).........((((((((((......)))))))))).....))))))) (-42.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAACAAAAACGAGGCCAGGAUUUUCGUCCCGACCUCUUACCUGGUUAGCUAAUAACUAGCUACUAUGAAUAUUAGCUUGGGGUAAAACAUCCACUGGAUGUGCCUGCGUUUCUAAUUUCUAGCGCAGUGCUAAACACGUCC ............((((.(.((((....)))).).)))).(((((.(..((((((((..((.......))..))))))))).)))))..((((((...))))))(((((((((..........))))))).))........... (-38.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 131 91 180 141 smit:SMT_161|5end_putative_folyl-polyglutamate_synthetase_105358..105588_POSITIVE 316 129 82 206 158 smit:SMT_1668|5end_K+_transport_system,_NAD-binding_component_1658288..1658518_NEGATIVE 313 48 1 188 137 smit:SMT_303|5end_hypothetical_protein_245364..245594_POSITIVE 305 70 29 64 22 smit:SMT_1531|5end_hypothetical_protein_1515997..1516227_NEGATIVE 293 102 61 52 7 smit:SMT_519|5end_glutathione_reductase_444884..445114_NEGATIVE 289 126 81 159 119 smit:SMT_139|5end_hypothetical_protein_90523..90753_POSITIVE 284 46 5 154 111 smit:SMT_489|5end_K01999_branched-chain_amino_acid_transport_system_substrate-binding_protein_423669..423899_POSITIVE 283 79 33 226 173 smit:SMT_1845|5end_K01191_alpha-mannosidase_1809663..1809893_POSITIVE 283 79 33 226 173 smit:SMT_114|5end_alpha-mannosidase_62804..63034_POSITIVE 282 140 104 57 22 smit:SMT_785|5end_hypothetical_protein_697242..697472_NEGATIVE 277 40 1 163 122 smit:SMT_864|5end_K07485_transposase_814322..814552_POSITIVE 274 137 97 231 200 smit:SMT_1132|5end_glutamate--cysteine_ligase,_putative,_truncated_1068108..1068338_NEGATIVE 272 132 92 195 157 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 267 88 43 87 39 smit:SMT_988|5end_N-acetylneuraminate_lyase_932889..933119_NEGATIVE 266 46 1 61 9 smit:SMT_1593|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1581417..1581647_POSITIVE 266 140 93 113 55 smit:SMT_1396|5end_uracil-DNA_glycosylase_1372064..1372294_POSITIVE 266 134 94 227 181 smit:SMT_1066|5end_holo-(acyl_carrier_protein)_synthase_1005411..1005641_POSITIVE 265 130 82 57 1 smit:SMT_2083|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1982411..1982641_POSITIVE 264 81 42 54 10 smit:SMT_106|5end_hypothetical_protein_51441..51671_POSITIVE 263 49 12 103 63 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 452 137 92 91 41 smit:SMT_1299|3end_MutT/NUDIX_family_protein_1262572..1262722_POSITIVE 377 58 20 128 82 smit:SMT_2112|3end_transcription-repair_coupling_factor_2000373..2000523_NEGATIVE 341 60 12 94 40 smit:SMT_159|3end_hypothetical_protein_104615..104765_POSITIVE 313 48 1 63 12 smit:SMT_302|3end_K07444_putative_N6-adenine-specific_DNA_methylase_245319..245469_POSITIVE 305 70 29 67 25 smit:SMT_1532|3end_hypothetical_protein_1515994..1516144_NEGATIVE 304 140 91 91 41 smit:SMT_1605|3end_hypothetical_protein_1595737..1595887_POSITIVE 293 102 61 55 10 smit:SMT_520|3end_glutathione_reductase_444881..445031_NEGATIVE 285 132 96 43 1 smit:SMT_478|3end_hypothetical_protein_predicted_by_Glimmer/Critica_415257..415407_POSITIVE 283 79 33 127 74 smit:SMT_1844|3end_hypothetical_protein_1809644..1809794_POSITIVE 283 79 33 127 74 smit:SMT_113|3end_hypothetical_protein_62785..62935_POSITIVE 282 140 104 60 25 smit:SMT_786|3end_hypothetical_protein_697239..697389_NEGATIVE 280 129 86 77 36 smit:SMT_1151|3end_histidyl-tRNA_synthetase_1095002..1095152_NEGATIVE 261 113 78 77 43 smit:SMT_1897|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1848766..1848916_NEGATIVE 259 131 94 83 42 smit:SMT_1795|3end_DNA_polymerase_III,_delta_subunit_1769185..1769335_NEGATIVE 259 140 91 68 4 smit:SMT_714|3end_hypothetical_protein_predicted_by_Glimmer/Critica_620890..621040_NEGATIVE 259 140 91 68 4 smit:SMT_696|3end_K03744_LemA_protein_606885..607035_NEGATIVE 258 50 8 148 90 smit:SMT_807|3end_hypothetical_protein_predicted_by_Glimmer/Critica_716708..716858_NEGATIVE 257 57 18 55 18 smit:SMT_1083|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1021001..1021151_POSITIVE 255 96 51 83 33 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 254 138 97 59 18 smit:SMT_207|3end_putative_two-component_sensor_histidine_kinase_138230..138380_NEGATIVE