Origin IGS: gcatagaactgattgaaagtcgatagcagctgaactctgtcgctgctgcaagtcttttcctgaaaatctttgattattttcaaaaatactggctttttcaatgttaatatggtaaaataaaaacaaagtaagcgttttcttgtttgctcatacaggggaatgcaggttcataacctcgttaaaaaatttttaggagggaatacaa .........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 ttgtattccctcctaaaaattttttaacgaggttatgaacctgcattcccctgtatgagcaaacaagaaaacgcttactttgtttttattttaccatattaacattgaaaaagccagtatttttgaaaataatcaaagattttcaggaaaagacttgcagcagcgacagagttcagctgctatcgactttcaatcagttctatgc Mask Tandem Repeat Region ================================================ gcatagaactgattgaaagtcgatagcagctgaactctgtcgctgctgcaagtcttttcctgaaaatctttgattattttcaaaaatactggctttttcaatgttaatatggtaaaataaaaacaaagtaagcgttttcttgtttgctcatacaggggaatgcaggttcataacctcgttaaaaaatttttaggagggaatacaa Find is-nt database================================================ Query_seq: SSA_0739:SSA_0740|SSA_0739:SSA_0740:Carbamate kinase, putative:C4-dicarboxylate anaerobic carrier, possible arginine transporter, putative:->->:722175..722379 205 gcatagaactgattgaaagtcgatagcagctgaactctgtcgctgctgcaagtcttttcctgaaaatctttgattattttcaaaaatactggctttttcaatgttaatatggtaaaataaaaacaaagtaagcgttttcttgtttgctcatacaggggaatgcaggttcataacctcgttaaaaaatttttaggagggaatacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0739:SSA_0740|SSA_0739:SSA_0740:Carbamate kinase, putative:C4-dicarboxylate anaerobic carrier, possible arginine transporter, putative:->->:722175..722379 205 gcatagaactgattgaaagtcgatagcagctgaactctgtcgctgctgcaagtcttttcctgaaaatctttgattattttcaaaaatactggctttttcaatgttaatatggtaaaataaaaacaaagtaagcgttttcttgtttgctcatacaggggaatgcaggttcataacctcgttaaaaaatttttaggagggaatacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0739:SSA_0740|SSA_0739:SSA_0740:Carbamate kinase, putative:C4-dicarboxylate anaerobic carrier, possible arginine transporter, putative:->->:722175..722379 205 gcatagaactgattgaaagtcgatagcagctgaactctgtcgctgctgcaagtcttttcctgaaaatctttgattattttcaaaaatactggctttttcaatgttaatatggtaaaataaaaacaaagtaagcgttttcttgtttgctcatacaggggaatgcaggttcataacctcgttaaaaaatttttaggagggaatacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcatagaactgattgaaagtcgatagcagctgaactctgtcgctgctgcaagtcttttcctgaaaatctttgattattttcaaaaatactggctttttcaatgttaatatggtaaaataaaaacaaagtaagcgttttcttgtttgctcatacaggggaatgcaggttcataacctcgttaaaaaatttttaggagggaatacaa Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: - Start: 3 End: 161 .. Y F Q N F T S L L Q V R D S S C T K E Q F D K I I K L F V P K K L T L I T F Y F C L L R K R T Q E Y L P M ............................................ Protein_Len: 42 Strand: - Start: 1 End: 126 C L V S Q F D I A A S S Q R Q Q L D K G S F R Q N N E F I S A K E I N I H Y F L F M ............................................................................... gcatagaactgattgaaagtcgatagcagctgaactctgtcgctgctgcaagtcttttcctgaaaatctttgattattttcaaaaatactggctttttcaatgttaatatggtaaaataaaaacaaagtaagcgttttcttgtttgctcatacaggggaatgcaggttcataacctcgttaaaaaatttttaggagggaatacaa 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: 84 Start: 73 End: 102 ........................................................................ATTGAAAAAGCCAGTATTTTTGAAAATAAT....................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcatagaactgattgaaagtcgatagcagctgaactctgtcgctgctgcaagtcttttcctgaaaatctttgattattttcaaaaatactggctttttcaatgttaatatggtaaaataaaaacaaagtaagcgttttcttgtttgctcatacaggggaatgcaggttcataacctcgttaaaaaatttttaggagggaatacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0739:SSA_0740|SSA_0739:SSA_0740:Carbamate kinase, putative:C4-dicarboxylate anaerobic carrier, possible arginine transporter, putative:->->:722175..722379 205 gcatagaactgattgaaagtcgatagcagctgaactctgtcgctgctgcaagtcttttcctgaaaatctttgattattttcaaaaatactggctttttcaatgttaatatggtaaaataaaaacaaagtaagcgttttcttgtttgctcatacaggggaatgcaggttcataacctcgttaaaaaatttttaggagggaatacaa Intra-Species Hit: Count: 1 Min: 1 Max: 205 Len: 205 Subject: NC_009009_SSA_0739_SSA_0740|Carbamate kinase, putative:C4-dicarboxylate anaerobic carrier, possible arginine transporter, putative|POSITIVE:POSITIVE|[722175,722379]|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 gcatagaactgattgaaagtcgatagcagctgaactctgtcgctgctgcaagtcttttcctgaaaatctttgattattttcaaaaatactggctttttcaatgttaatatggtaaaataaaaacaaagtaagcgttttcttgtttgctcatacaggggaatgcaggttcataacctcgttaaaaaatttttaggagggaatacaa gcatagaactgattgaaagtcgatagcagctgaactctgtcgctgctgcaagtcttttcctgaaaatctttgattattttcaaaaatactggctttttcaatgttaatatggtaaaataaaaacaaagtaagcgttttcttgtttgctcatacaggggaatgcaggttcataacctcgttaaaaaatttttaggagggaatacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAUAGAACUGAUUGAAAGUCGAUAGCAGCUGAACUCUGUCGCUGCUGCAAGUCUUUUCCUGAAAAUCUUUGAUUAUUUUCAAAAAUACUGGCUUUUUCAAUGUUAAUAUGGUAAAAUAAAAACAAAGUAAGCGUUUUCUUGUUUGCUCAUACAGGGGAAUGCAGGUUCAUAACCUCGUUAAAAAAUUUUUAGGAGGGAAUACAA .....(((((....(((((((..(((((((.((......)))))))))..(((.((((..(((((((........))))))))))).))))))))))....((((..(((......)))..))))......(((((..(((((........)))))..))))).)))))....((((.(((((.....)))))))))........ (-47.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUAUUCCCUCCUAAAAAUUUUUUAACGAGGUUAUGAACCUGCAUUCCCCUGUAUGAGCAAACAAGAAAACGCUUACUUUGUUUUUAUUUUACCAUAUUAACAUUGAAAAAGCCAGUAUUUUUGAAAAUAAUCAAAGAUUUUCAGGAAAAGACUUGCAGCAGCGACAGAGUUCAGCUGCUAUCGACUUUCAAUCAGUUCUAUGC ...(((..((((.((((.....))))..))))..)))...............((((((((......(((((((.......)))))))................(((((((..((.(((.(((((((((((........)))))))))))...))).)).(((((((......)).))))).......)))))))..)))).)))) (-37.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 421 59 15 204 163 NC_009009:SSA_1441|5end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1445183..1445413_NEGATIVE 396 55 20 50 15 NC_009009:SSA_1082|5end_PTS_system,_fructose_specific_II_ABC_components,_putative_1099186..1099416_POSITIVE 350 53 17 166 129 NC_009009:SSA_2063|5end_Aminopeptidase_PepS,_putative_2064857..2065087_NEGATIVE 346 50 9 68 21 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 343 55 12 70 26 NC_009009:SSA_0548|5end_Alanine_racemase,_putative_542340..542570_POSITIVE 328 60 12 179 135 NC_009009:SSA_0972|5end_hypothetical_protein_979973..980203_POSITIVE 325 65 21 66 8 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 325 49 1 195 140 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 316 62 25 179 144 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 311 63 22 166 113 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 310 63 28 45 9 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 310 49 2 202 150 NC_009009:SSA_1469|5end_Shikimate_dehydrogenase,_putative_1476317..1476547_NEGATIVE 304 53 18 173 139 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 301 64 21 226 174 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 298 62 22 58 20 NC_009009:SSA_0781|5end_Mannose-6-phosphate_isomerase,_putative_765373..765603_POSITIVE 297 49 1 195 149 NC_009009:SSA_1324|5end_Ceramide_glucosyltransferase,_putative_1341618..1341848_NEGATIVE 296 59 19 79 39 NC_009009:SSA_1154|5end_hypothetical_protein_1182661..1182891_POSITIVE 296 50 6 68 22 NC_009009:SSA_0773|5end_PTS_enzyme_I,_putative_752603..752833_POSITIVE 296 49 9 160 117 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 294 54 18 31 1 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 55 20 53 18 NC_009009:SSA_1081|3end_1-phosphofructokinase,_putative_1099269..1099419_POSITIVE 350 53 17 144 107 NC_009009:SSA_2064|3end_hypothetical_protein_2064879..2065029_NEGATIVE 343 55 12 83 39 NC_009009:SSA_0547|3end_Acyl_carrier_protein_synthase,_putative_542433..542583_POSITIVE 325 65 21 76 18 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 312 51 19 43 6 NC_009009:SSA_1856|3end_hypothetical_protein_1852077..1852227_NEGATIVE 306 68 26 75 29 NC_009009:SSA_0177|3end_DNA-directed_RNA_polymerase_I,_beta_chain_(160_kDa_subunit),_putative_182132..182282_POSITIVE 305 69 28 145 104 NC_009009:SSA_0999|3end_Biotin--[acetyl-CoA-carboxylase]_ligase,_putative_998781..998931_NEGATIVE 296 59 19 86 46 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 296 60 17 87 26 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 296 50 6 66 20 NC_009009:SSA_0772|3end_Histidine-containing_phosphocarrier_protein_of_the_PTS,_putative_752681..752831_POSITIVE 294 54 13 151 115 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 292 61 26 110 75 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 290 49 10 135 96 NC_009009:SSA_1418|3end_Conserved_uncharacterized_protein_1428139..1428289_NEGATIVE 287 60 19 96 52 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 283 77 36 98 49 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 282 44 1 147 111 NC_009009:SSA_1595|3end_Tellurite_resistance,_putative_1600951..1601101_NEGATIVE 281 61 21 122 73 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE 281 59 11 144 80 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 280 50 9 127 86 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 280 48 8 135 93 NC_009009:SSA_0794|3end_Zn-dependent_protease,_putative_776695..776845_POSITIVE