Origin IGS: catatgataaagcagtaagtgataagaaaaaatgaactctttggaatctaatttttgtttggtcagaaattaggttcaaagagtttttttattaattaagtctgtctgcctagctactatgtgattttggtacttgagttttataaaaagtagaattttgtgatagaataggggagtcggaggattttttt .........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 aaaaaaatcctccgactcccctattctatcacaaaattctactttttataaaactcaagtaccaaaatcacatagtagctaggcagacagacttaattaataaaaaaactctttgaacctaatttctgaccaaacaaaaattagattccaaagagttcattttttcttatcacttactgctttatcatatg Mask Tandem Repeat Region ================================================ catatgataaagcagtaagtgataagaaaaaatgaactctttggaatctaatttttgtttggtcagaaattaggttcaaagagtttttttattaattaagtctgtctgcctagctactatgtgattttggtacttgagttttataaaaagtagaattttgtgatagaataggggagtcggaggattttttt Find is-nt database================================================ Query_seq: SSA_0750:SSA_0751|SSA_0750:SSA_0751:hypothetical protein:Oligoendopeptidase F, putative:->->:732316..732506 191 catatgataaagcagtaagtgataagaaaaaatgaactctttggaatctaatttttgtttggtcagaaattaggttcaaagagtttttttattaattaagtctgtctgcctagctactatgtgattttggtacttgagttttataaaaagtagaattttgtgatagaataggggagtcggaggattttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0750:SSA_0751|SSA_0750:SSA_0751:hypothetical protein:Oligoendopeptidase F, putative:->->:732316..732506 191 catatgataaagcagtaagtgataagaaaaaatgaactctttggaatctaatttttgtttggtcagaaattaggttcaaagagtttttttattaattaagtctgtctgcctagctactatgtgattttggtacttgagttttataaaaagtagaattttgtgatagaataggggagtcggaggattttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0750:SSA_0751|SSA_0750:SSA_0751:hypothetical protein:Oligoendopeptidase F, putative:->->:732316..732506 191 catatgataaagcagtaagtgataagaaaaaatgaactctttggaatctaatttttgtttggtcagaaattaggttcaaagagtttttttattaattaagtctgtctgcctagctactatgtgattttggtacttgagttttataaaaagtagaattttgtgatagaataggggagtcggaggattttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 catatgataaagcagtaagtgataagaaaaaatgaactctttggaatctaatttttgtttggtcagaaattaggttcaaagagtttttttattaattaagtctgtctgcctagctactatgtgattttggtacttgagttttataaaaagtagaattttgtgatagaataggggagtcggaggattttttt Predict ORF larger than 30AA ================================================ catatgataaagcagtaagtgataagaaaaaatgaactctttggaatctaatttttgtttggtcagaaattaggttcaaagagtttttttattaattaagtctgtctgcctagctactatgtgattttggtacttgagttttataaaaagtagaattttgtgatagaataggggagtcggaggattttttt 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================================================ catatgataaagcagtaagtgataagaaaaaatgaactctttggaatctaatttttgtttggtcagaaattaggttcaaagagtttttttattaattaagtctgtctgcctagctactatgtgattttggtacttgagttttataaaaagtagaattttgtgatagaataggggagtcggaggattttttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.6 Tail_Score: -5.87996 Start: 37 End: 83 Full_Region: ATAAGAAAAAATGAA CTCTTTGGAATCTAATTTTTG TTTGGT CAGAAATTAGGTTCAAAGAG TTTTTTTATTAATTA ....................................CTCTTTGGAATCTAATTTTTGTTTGGTCAGAAATTAGGTTCAAAGAG............................................................................................................ TransTerm Strand: - Conf: 68 HP_score: -6.2 Tail_Score: -4.05512 Start: 37 End: 83 Full_Region: taattaataaaaaaa ctctttgaacctaatttctg accaaa caaaaattagattccaaagag ttcattttttcttat ....................................ctctttgaacctaatttctgaccaaacaaaaattagattccaaagag............................................................................................................ Find igs database================================================ Query_seq: SSA_0750:SSA_0751|SSA_0750:SSA_0751:hypothetical protein:Oligoendopeptidase F, putative:->->:732316..732506 191 catatgataaagcagtaagtgataagaaaaaatgaactctttggaatctaatttttgtttggtcagaaattaggttcaaagagtttttttattaattaagtctgtctgcctagctactatgtgattttggtacttgagttttataaaaagtagaattttgtgatagaataggggagtcggaggattttttt Intra-Species Hit: Count: 1 Min: 1 Max: 184 Len: 184 Subject: NC_009009_SSA_0750_SSA_0751|hypothetical protein:Oligoendopeptidase F, putative|POSITIVE:POSITIVE|[732316,732506]|191 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 catatgataaagcagtaagtgataagaaaaaatgaactctttggaatctaatttttgtttggtcagaaattaggttcaaagagnnnnnnnattaattaagtctgtctgcctagctactatgtgattttggtacttgagttttataaaaagtagaattttgtgatagaataggggagtcggagga....... catatgataaagcagtaagtgataagaaaaaatgaactctttggaatctaatttttgtttggtcagaaattaggttcaaagagtttttttattaattaagtctgtctgcctagctactatgtgattttggtacttgagttttataaaaagtagaattttgtgatagaataggggagtcggagga....... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAUGAUAAAGCAGUAAGUGAUAAGAAAAAAUGAACUCUUUGGAAUCUAAUUUUUGUUUGGUCAGAAAUUAGGUUCAAAGAGUUUUUUUAUUAAUUAAGUCUGUCUGCCUAGCUACUAUGUGAUUUUGGUACUUGAGUUUUAUAAAAAGUAGAAUUUUGUGAUAGAAUAGGGGAGUCGGAGGA ...............(((.((((((((......((((((((((.(((((((((((((......))))))))))))))))))))))))))))))).)))..((((.((.(((.((......)).((((((.(((..(((((((((.....))))))))).))).)))))).))).)).))))... (-46.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUCCGACUCCCCUAUUCUAUCACAAAAUUCUACUUUUUAUAAAACUCAAGUACCAAAAUCACAUAGUAGCUAGGCAGACAGACUUAAUUAAUAAAAAAACUCUUUGAACCUAAUUUCUGACCAAACAAAAAUUAGAUUCCAAAGAGUUCAUUUUUUCUUAUCACUUACUGCUUUAUCAUAUG ...............................................................((((......((((((..((...(((..((.(((..(((((((((((.(((((((.((......)).))))))).)).)))))))))..)))))..)))...))..)))))).....)))) (-23.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 133 102 69 39 NC_009009:SSA_2045|5end_Reductase,_putative_2048948..2049178_NEGATIVE 262 77 37 55 17 NC_009009:SSA_1509|5end_Polysaccharide_biosynthesis_protein/_rhamnosyltransferase,_putative_1514191..1514421_NEGATIVE 257 47 6 229 188 NC_009009:SSA_1643|5end_hypothetical_protein_1645269..1645499_NEGATIVE 250 140 98 68 15 NC_009009:SSA_2284|5end_Histidyl-tRNA_synthetase,_putative_2287272..2287502_NEGATIVE 248 90 48 50 8 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 246 138 102 132 85 NC_009009:SSA_2316|5end_General_secretory_pathway_protein_F,_putative_2318342..2318572_NEGATIVE 245 77 32 81 42 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 241 144 106 215 173 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 238 110 61 69 12 NC_009009:SSA_1799|5end_Acetyltransferase,_putative_1781025..1781255_NEGATIVE 232 139 95 63 21 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 232 62 31 150 121 NC_009009:SSA_0264|5end_PEP_phosphonomutase-like_protein,_putative_258400..258630_POSITIVE 228 130 82 144 95 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 225 137 102 83 51 NC_009009:SSA_1418|5end_Conserved_uncharacterized_protein_1428927..1429157_NEGATIVE 225 136 105 82 47 NC_009009:SSA_0330|5end_hypothetical_protein_323799..324029_POSITIVE 224 136 99 61 20 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 223 138 99 39 1 NC_009009:SSA_2069|5end_Prolyl-tRNA_synthetase,_putative_2073252..2073482_NEGATIVE 223 130 102 221 187 NC_009009:SSA_1491|5end_Methionine_aminopeptidase_A,_putative_1497637..1497867_NEGATIVE 222 179 132 174 142 NC_009009:SSA_0423|5end_hypothetical_protein_421347..421577_NEGATIVE 221 132 100 77 42 NC_009009:SSA_0568|5end_Aspartyl-tRNA_synthetase_1,_putative_561674..561904_POSITIVE 221 140 100 157 124 NC_009009:SSA_0112|5end_50S_ribosomal_protein_L22,_putative_110965..111195_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 90 44 63 14 NC_009009:SSA_0750|3end_hypothetical_protein_732255..732405_POSITIVE 265 133 102 60 30 NC_009009:SSA_2046|3end_Uridine_phosphorylase,_putative_2048957..2049107_NEGATIVE 262 77 37 58 20 NC_009009:SSA_1510|3end_Rhamnosyltransferase,_putative_1514188..1514338_NEGATIVE 246 138 102 128 81 NC_009009:SSA_2317|3end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2318346..2318496_NEGATIVE 245 77 32 84 45 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 241 115 72 107 59 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 237 110 66 57 1 NC_009009:SSA_1800|3end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1781037..1781187_NEGATIVE 228 130 82 142 93 NC_009009:SSA_1403|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1416222..1416372_NEGATIVE 228 138 102 74 27 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE 224 136 99 76 35 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 223 120 71 122 62 NC_009009:SSA_0613|3end_Glucosyltransferase,_putative_606633..606783_POSITIVE 221 140 100 145 112 NC_009009:SSA_0111|3end_30S_ribosomal_protein_S19,_putative_111033..111183_POSITIVE 217 94 57 79 41 NC_009009:SSA_1147|3end_Beta-glucosides_PTS,_EIIB,_putative_1177152..1177302_POSITIVE 216 135 95 119 71 NC_009009:SSA_1433|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1439933..1440083_NEGATIVE 214 123 91 132 100 NC_009009:SSA_1270|3end_Flavodoxin_1293476..1293626_NEGATIVE 213 139 101 134 95 NC_009009:SSA_2287|3end_50S_ribosomal_protein_L32,_putative_2290083..2290233_POSITIVE 213 137 98 103 64 NC_009009:SSA_1617|3end_hypothetical_protein_1620436..1620586_NEGATIVE 212 78 37 146 102 NC_009009:SSA_1864|3end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1859410..1859560_NEGATIVE 212 174 131 69 29 NC_009009:SSA_1217|3end_Conserved_uncharacterized_protein_1239736..1239886_POSITIVE 212 115 71 52 2 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE