Origin IGS: gctcaagatacaaagactgtaaaaagctcacagtgcatacaaaggcaaccacatccgtaaactactgaattagtaacggctgtggaaaaatagggaatcttaaaaagaagcttcagcttcttggaagattcatctttttcgcacagagcttagggcgttttccattcagcgcatgggaaagagtatataagacaagattttagaggagaagact .........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 agtcttctcctctaaaatcttgtcttatatactctttcccatgcgctgaatggaaaacgccctaagctctgtgcgaaaaagatgaatcttccaagaagctgaagcttctttttaagattccctatttttccacagccgttactaattcagtagtttacggatgtggttgcctttgtatgcactgtgagctttttacagtctttgtatcttgagc Mask Tandem Repeat Region ================================================ gctcaagatacaaagactgtaaaaagctcacagtgcatacaaaggcaaccacatccgtaaactactgaattagtaacggctgtggaaaaatagggaatcttaaaaagaagcttcagcttcttggaagattcatctttttcgcacagagcttagggcgttttccattcagcgcatgggaaagagtatataagacaagattttagaggagaagact Find is-nt database================================================ Query_seq: SSA_1005:SSA_1006|SSA_1005:SSA_1006:Sugar ABC transporter, permease protein, putative:Dextransucrase, putative:->->:1007002..1007215 214 gctcaagatacaaagactgtaaaaagctcacagtgcatacaaaggcaaccacatccgtaaactactgaattagtaacggctgtggaaaaatagggaatcttaaaaagaagcttcagcttcttggaagattcatctttttcgcacagagcttagggcgttttccattcagcgcatgggaaagagtatataagacaagattttagaggagaagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1005:SSA_1006|SSA_1005:SSA_1006:Sugar ABC transporter, permease protein, putative:Dextransucrase, putative:->->:1007002..1007215 214 gctcaagatacaaagactgtaaaaagctcacagtgcatacaaaggcaaccacatccgtaaactactgaattagtaacggctgtggaaaaatagggaatcttaaaaagaagcttcagcttcttggaagattcatctttttcgcacagagcttagggcgttttccattcagcgcatgggaaagagtatataagacaagattttagaggagaagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1005:SSA_1006|SSA_1005:SSA_1006:Sugar ABC transporter, permease protein, putative:Dextransucrase, putative:->->:1007002..1007215 214 gctcaagatacaaagactgtaaaaagctcacagtgcatacaaaggcaaccacatccgtaaactactgaattagtaacggctgtggaaaaatagggaatcttaaaaagaagcttcagcttcttggaagattcatctttttcgcacagagcttagggcgttttccattcagcgcatgggaaagagtatataagacaagattttagaggagaagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctcaagatacaaagactgtaaaaagctcacagtgcatacaaaggcaaccacatccgtaaactactgaattagtaacggctgtggaaaaatagggaatcttaaaaagaagcttcagcttcttggaagattcatctttttcgcacagagcttagggcgttttccattcagcgcatgggaaagagtatataagacaagattttagaggagaagact Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 69 End: 200 .................................................................... M S N G C G K I G N L K K K L Q L L G R F I F F A Q S L G R F P F S A W E R V Y K T R F .............. Protein_Len: 48 Strand: - Start: 6 End: 146 ..... * S V F V T F L E C H M C L C G C G Y V V S N T V A T S F Y P I K F L L K L K K S S E D K E C M .................................................................... gctcaagatacaaagactgtaaaaagctcacagtgcatacaaaggcaaccacatccgtaaactactgaattagtaacggctgtggaaaaatagggaatcttaaaaagaagcttcagcttcttggaagattcatctttttcgcacagagcttagggcgttttccattcagcgcatgggaaagagtatataagacaagattttagaggagaagact 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================================================ gctcaagatacaaagactgtaaaaagctcacagtgcatacaaaggcaaccacatccgtaaactactgaattagtaacggctgtggaaaaatagggaatcttaaaaagaagcttcagcttcttggaagattcatctttttcgcacagagcttagggcgttttccattcagcgcatgggaaagagtatataagacaagattttagaggagaagact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 52 HP_score: -4.5 Tail_Score: -3.35695 Start: 49 End: 85 Full_Region: agattccctattttt ccacagccgttacta attcag tagtttacggatgtgg ttgcctttgtatgca ................................................ccacagccgttactaattcagtagtttacggatgtgg................................................................................................................................. TransTerm Strand: - Conf: 81 HP_score: -6.7 Tail_Score: -4.67234 Start: 107 End: 120 Full_Region: agatgaatcttccaa gaagc tgaa gcttc tttttaagattccct ..........................................................................................................gaagctgaagcttc.............................................................................................. Find igs database================================================ Query_seq: SSA_1005:SSA_1006|SSA_1005:SSA_1006:Sugar ABC transporter, permease protein, putative:Dextransucrase, putative:->->:1007002..1007215 214 gctcaagatacaaagactgtaaaaagctcacagtgcatacaaaggcaaccacatccgtaaactactgaattagtaacggctgtggaaaaatagggaatcttaaaaagaagcttcagcttcttggaagattcatctttttcgcacagagcttagggcgttttccattcagcgcatgggaaagagtatataagacaagattttagaggagaagact Intra-Species Hit: Count: 1 Min: 1 Max: 214 Len: 214 Subject: NC_009009_SSA_1005_SSA_1006|Sugar ABC transporter, permease protein, putative:Dextransucrase, putative|POSITIVE:POSITIVE|[1007002,1007215]|214 HSP 1 e-value: 1.0E-118 bit: 424.0 Len: 214 Query Start:1 Query End:214 Subject Strand: POSITIVE Subject Start: 1 Subject End: 214 gctcaagatacaaagactgtaaaaagctcacagtgcatacaaaggcaaccacatccgtaaactactgaattagtaacggctgtggaaaaatagggaatcttaaaaagaagcttcagcttcttggaagattcatctttttcgcacagagcttagggcgttttccattcagcgcatgggaaagagtatataagacaagattttagaggagaagact gctcaagatacaaagactgtaaaaagctcacagtgcatacaaaggcaaccacatccgtaaactactgaattagtaacggctgtggaaaaatagggaatcttaaaaagaagcttcagcttcttggaagattcatctttttcgcacagagcttagggcgttttccattcagcgcatgggaaagagtatataagacaagattttagaggagaagact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUCAAGAUACAAAGACUGUAAAAAGCUCACAGUGCAUACAAAGGCAACCACAUCCGUAAACUACUGAAUUAGUAACGGCUGUGGAAAAAUAGGGAAUCUUAAAAAGAAGCUUCAGCUUCUUGGAAGAUUCAUCUUUUUCGCACAGAGCUUAGGGCGUUUUCCAUUCAGCGCAUGGGAAAGAGUAUAUAAGACAAGAUUUUAGAGGAGAAGACU ((((....((((.....))))..((((((...((((............(((((.((((..((((......)))).)))).)))))..(((.((((((((((...(((((((....)))))))..))))))).))).))).)))).)))))).)))).((((((((.......)))))))).................................. (-59.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCUUCUCCUCUAAAAUCUUGUCUUAUAUACUCUUUCCCAUGCGCUGAAUGGAAAACGCCCUAAGCUCUGUGCGAAAAAGAUGAAUCUUCCAAGAAGCUGAAGCUUCUUUUUAAGAUUCCCUAUUUUUCCACAGCCGUUACUAAUUCAGUAGUUUACGGAUGUGGUUGCCUUUGUAUGCACUGUGAGCUUUUUACAGUCUUUGUAUCUUGAGC .......................((((.((((......((((.......))))...((.....((((((.(((((..((((..(((((((..(((((((....)))))))...))))))).........(((((.((((.((((......))))..)))).)))))....))))...)))))...))))))......))....))))..)))). (-53.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 158 111 211 164 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 362 150 105 177 138 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 348 167 132 202 167 NC_009009:SSA_1226|5end_ParC,_putative_1251233..1251463_NEGATIVE 345 178 133 158 106 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 344 176 132 99 62 NC_009009:SSA_0636|5end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625184..625414_POSITIVE 338 139 91 86 40 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 317 176 133 65 15 NC_009009:SSA_0114|5end_50S_ribosomal_protein_L16,_putative_111979..112209_POSITIVE 309 178 132 229 198 NC_009009:SSA_1570|5end_hypothetical_protein_1572659..1572889_POSITIVE 308 170 121 76 20 NC_009009:SSA_0026|5end_Fatty_acid/phospholipid_synthesis_protein_plsX,_putative_30473..30703_POSITIVE 303 176 131 51 5 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 302 173 132 165 118 NC_009009:SSA_1952|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1949624..1949854_NEGATIVE 302 178 134 67 12 NC_009009:SSA_1587|5end_hypothetical_protein_1589086..1589316_NEGATIVE 302 176 133 230 187 NC_009009:SSA_1250|5end_Conserved_uncharacterized_protein,_putative_1274512..1274742_NEGATIVE 299 176 131 166 122 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 299 177 135 212 169 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 297 158 112 48 7 NC_009009:SSA_0078|5end_N-acetylneuraminate_lyase,_putative_81904..82134_POSITIVE 296 157 111 200 151 NC_009009:SSA_2346|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2348546..2348776_NEGATIVE 293 155 114 201 157 NC_009009:SSA_2318|5end_PilB-like_pili_biogenesis_ATPase,_putative_2321094..2321324_NEGATIVE 293 176 143 55 22 NC_009009:SSA_2167|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2167371..2167601_NEGATIVE 292 86 43 190 146 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 344 176 132 70 33 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 320 159 111 87 37 NC_009009:SSA_1244|3end_hypothetical_protein_1268465..1268615_NEGATIVE 317 176 133 61 11 NC_009009:SSA_0113|3end_30S_ribosomal_protein_S3,_putative_112055..112205_POSITIVE 312 172 132 113 71 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 309 178 132 120 89 NC_009009:SSA_1569|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1572630..1572780_POSITIVE 308 170 121 70 14 NC_009009:SSA_0025|3end_DNA_repair_protein_recO,_putative_30547..30697_POSITIVE 303 178 135 142 94 NC_009009:SSA_0200|3end_Bifunctional_folate_synthesis_protein,_putative_199810..199960_POSITIVE 302 173 132 147 100 NC_009009:SSA_1953|3end_NifU_family_protein,_putative_1949642..1949792_NEGATIVE 296 157 111 99 50 NC_009009:SSA_2347|3end_Coenzyme_F390_synthetase,_putative_2348647..2348797_NEGATIVE 292 86 43 125 81 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 292 145 106 44 5 NC_009009:SSA_0079|3end_ROK_family_protein,_putative_83819..83969_POSITIVE 290 156 115 74 36 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 289 60 18 70 9 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 289 156 114 84 40 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 289 176 132 141 94 NC_009009:SSA_0492|3end_NADH-dependent_flavin_oxidoreductase,_putative_492771..492921_POSITIVE 288 81 41 57 21 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 283 85 49 42 6 NC_009009:SSA_1005|3end_Sugar_ABC_transporter,_permease_protein,_putative_1006941..1007091_POSITIVE 282 166 122 54 1 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 281 156 113 141 95 NC_009009:SSA_1423|3end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1431561..1431711_NEGATIVE 276 150 105 80 37 NC_009009:SSA_0983|3end_Conserved_uncharacterized_protein_986945..987095_POSITIVE