Origin IGS: tatataaaatagtaaataagctagccgaccatttgaagctagcttatttatctaacaagcagcaatggaaagtttcagttttcaaaaaaacgttatttagaaaaatcactgttttcattgctcaggagaaaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttttctcctgagcaatgaaaacagtgatttttctaaataacgtttttttgaaaactgaaactttccattgctgcttgttagataaataagctagcttcaaatggtcggctagcttatttactattttatata Mask Tandem Repeat Region ================================================ tatataaaatagtaaataagctagccgaccatttgaagctagcttatttatctaacaagcagcaatggaaagtttcagttttcaaaaaaacgttatttagaaaaatcactgttttcattgctcaggagaaaaat Find is-nt database================================================ Query_seq: SSA_0540:SSA_0541|SSA_0540:SSA_0541:Glycerol uptake facilitator protein, putative:Acetate kinase, putative:->->:535809..535942 134 tatataaaatagtaaataagctagccgaccatttgaagctagcttatttatctaacaagcagcaatggaaagtttcagttttcaaaaaaacgttatttagaaaaatcactgttttcattgctcaggagaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0540:SSA_0541|SSA_0540:SSA_0541:Glycerol uptake facilitator protein, putative:Acetate kinase, putative:->->:535809..535942 134 tatataaaatagtaaataagctagccgaccatttgaagctagcttatttatctaacaagcagcaatggaaagtttcagttttcaaaaaaacgttatttagaaaaatcactgttttcattgctcaggagaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0540:SSA_0541|SSA_0540:SSA_0541:Glycerol uptake facilitator protein, putative:Acetate kinase, putative:->->:535809..535942 134 tatataaaatagtaaataagctagccgaccatttgaagctagcttatttatctaacaagcagcaatggaaagtttcagttttcaaaaaaacgttatttagaaaaatcactgttttcattgctcaggagaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatataaaatagtaaataagctagccgaccatttgaagctagcttatttatctaacaagcagcaatggaaagtttcagttttcaaaaaaacgttatttagaaaaatcactgttttcattgctcaggagaaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 9 End: 134 ........ M V N K L A D H L K L A Y L S N K Q Q W K V S V F K K T L F R K I T V F I A Q E K N tatataaaatagtaaataagctagccgaccatttgaagctagcttatttatctaacaagcagcaatggaaagtttcagttttcaaaaaaacgttatttagaaaaatcactgttttcattgctcaggagaaaaat 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================================================ tatataaaatagtaaataagctagccgaccatttgaagctagcttatttatctaacaagcagcaatggaaagtttcagttttcaaaaaaacgttatttagaaaaatcactgttttcattgctcaggagaaaaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 61 HP_score: -4.4 Tail_Score: -4.11862 Start: 17 End: 46 Full_Region: tgcttgttagataaa taagctagct tcaaatggtc ggctagctta tttactattttatat ................taagctagcttcaaatggtcggctagctta........................................................................................ Find igs database================================================ Query_seq: SSA_0540:SSA_0541|SSA_0540:SSA_0541:Glycerol uptake facilitator protein, putative:Acetate kinase, putative:->->:535809..535942 134 tatataaaatagtaaataagctagccgaccatttgaagctagcttatttatctaacaagcagcaatggaaagtttcagttttcaaaaaaacgttatttagaaaaatcactgttttcattgctcaggagaaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: NC_009009_SSA_0540_SSA_0541|Glycerol uptake facilitator protein, putative:Acetate kinase, putative|POSITIVE:POSITIVE|[535809,535942]|134 HSP 1 e-value: 6.0E-58 bit: 224.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 tatataaaatagtaaataagctagccgaccatttgaagctagcttatttatctaacaagcagcaatggaaagtttcagttttcnnnnnnncgttatttagaaaaatcactgttttcattgctcaggagaaaaat tatataaaatagtaaataagctagccgaccatttgaagctagcttatttatctaacaagcagcaatggaaagtttcagttttcaaaaaaacgttatttagaaaaatcactgttttcattgctcaggagaaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAUAAAAUAGUAAAUAAGCUAGCCGACCAUUUGAAGCUAGCUUAUUUAUCUAACAAGCAGCAAUGGAAAGUUUCAGUUUUCAAAAAAACGUUAUUUAGAAAAAUCACUGUUUUCAUUGCUCAGGAGAAAAAU .........(((((((((((((((((((....)))..))))))))))))).)))....(.(((((((((((.......(((((.(((........))).))))).......))))))))))))........... (-31.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUCUCCUGAGCAAUGAAAACAGUGAUUUUUCUAAAUAACGUUUUUUUGAAAACUGAAACUUUCCAUUGCUGCUUGUUAGAUAAAUAAGCUAGCUUCAAAUGGUCGGCUAGCUUAUUUACUAUUUUAUAUA ............(((((((.(((((((....((((.(((........))).))))))))....))).)))))))......(((.((((((((((((((((....))..)))))))))))))))))......... (-30.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 70 21 229 185 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 285 69 21 163 104 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 267 63 22 55 13 NC_009009:SSA_0142|5end_hypothetical_protein_137230..137460_POSITIVE 264 68 21 170 110 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 261 66 29 194 161 NC_009009:SSA_1463|5end_Shikimate_kinase,_putative_1470240..1470470_NEGATIVE 255 69 21 227 180 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 253 60 19 205 166 NC_009009:SSA_1497|5end_DCMP_deaminase,_putative_1503535..1503765_NEGATIVE 253 44 20 63 39 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 245 60 19 66 21 NC_009009:SSA_1417|5end_SAM-dependent_methyltransferase,_putative_1427993..1428223_NEGATIVE 245 44 11 150 116 NC_009009:SSA_0257|5end_N-acetylmuramidase/lysin,_putative_248878..249108_POSITIVE 241 70 22 72 33 NC_009009:SSA_0879|5end_Cell_division_regulator,_negative_regulator_of_FtsZ_septation_ring_formation,_putative_873632..873862_POSITIVE 240 68 21 67 13 NC_009009:SSA_1573|5end_hypothetical_protein_1576536..1576766_NEGATIVE 236 65 23 50 16 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 235 76 37 122 86 NC_009009:SSA_0839|5end_hypothetical_protein_826751..826981_POSITIVE 234 57 19 59 25 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 230 68 22 225 182 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 230 84 52 86 46 NC_009009:SSA_1078|5end_hypothetical_protein_1095742..1095972_POSITIVE 228 64 23 42 1 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 228 44 19 149 125 NC_009009:SSA_1120|5end_Two-component_sensor_kinase_(with_C-terminal_ATPase_domain),_putative_1145222..1145452_POSITIVE 228 69 21 206 150 NC_009009:SSA_0912|5end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_923100..923330_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 54 11 81 38 NC_009009:SSA_0540|3end_Glycerol_uptake_facilitator_protein,_putative_535748..535898_POSITIVE 262 68 31 149 109 NC_009009:SSA_0145|3end_Transcriptional_regulator,_TetR_family,_putative_138778..138928_NEGATIVE 254 45 21 142 113 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 253 44 20 70 46 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 235 76 37 120 84 NC_009009:SSA_0838|3end_GtfB,_putative_826829..826979_POSITIVE 234 57 19 59 25 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 230 84 52 93 53 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 230 64 26 107 74 NC_009009:SSA_0639|3end_hypothetical_protein_627733..627883_NEGATIVE 229 64 21 137 107 NC_009009:SSA_0416|3end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase,_putative_414222..414372_POSITIVE 228 68 21 43 4 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 227 80 36 146 82 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 226 78 36 50 7 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 222 55 20 54 18 NC_009009:SSA_1614|3end_Acetyltransferase,_GNAT_family,_putative_1617476..1617626_NEGATIVE 220 78 31 102 41 NC_009009:SSA_1280|3end_hypothetical_protein_1301108..1301258_NEGATIVE 218 75 40 131 87 NC_009009:SSA_1353|3end_hypothetical_protein_1367974..1368124_NEGATIVE 216 130 97 132 91 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 216 55 20 30 3 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 216 75 31 148 89 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 214 60 16 130 82 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 214 44 20 128 108 NC_009009:SSA_1350|3end_hypothetical_protein_1366945..1367095_NEGATIVE