Origin IGS: attatcacaacctttctaaaattaacctctctaaccttattatatcaaaaagataccggtttcacaatcttaaaattgttatattttcagaaaattaactttcgcacaaagctgtattttcgaagcgatgagacagcggtagtatagctttttaggctgtataagaatttttgaaaatctcgagcaaatttcttgtaaacgctcacaggagatgatatactgttctagtaaattataaattaaggtaggactattctt .........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 aagaatagtcctaccttaatttataatttactagaacagtatatcatctcctgtgagcgtttacaagaaatttgctcgagattttcaaaaattcttatacagcctaaaaagctatactaccgctgtctcatcgcttcgaaaatacagctttgtgcgaaagttaattttctgaaaatataacaattttaagattgtgaaaccggtatctttttgatataataaggttagagaggttaattttagaaaggttgtgataat Mask Tandem Repeat Region ================================================ attatcacaacctttctaaaattaacctctctaaccttattatatcaaaaagataccggtttcacaatcttaaaattgttatattttcagaaaattaactttcgcacaaagctgtattttcgaagcgatgagacagcggtagtatagctttttaggctgtataagaatttttgaaaatctcgagcaaatttcttgtaaacgctcacaggagatgatatactgttctagtaaattataaattaaggtaggactattctt Find is-nt database================================================ Query_seq: SSA_1126:SSA_1127|SSA_1126:SSA_1127:Thiamine biosynthesis lipoprotein, putative:H2O-forming NADH dehydrogenase, putative:<-->:1151613..1151870 258 attatcacaacctttctaaaattaacctctctaaccttattatatcaaaaagataccggtttcacaatcttaaaattgttatattttcagaaaattaactttcgcacaaagctgtattttcgaagcgatgagacagcggtagtatagctttttaggctgtataagaatttttgaaaatctcgagcaaatttcttgtaaacgctcacaggagatgatatactgttctagtaaattataaattaaggtaggactattctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1126:SSA_1127|SSA_1126:SSA_1127:Thiamine biosynthesis lipoprotein, putative:H2O-forming NADH dehydrogenase, putative:<-->:1151613..1151870 258 attatcacaacctttctaaaattaacctctctaaccttattatatcaaaaagataccggtttcacaatcttaaaattgttatattttcagaaaattaactttcgcacaaagctgtattttcgaagcgatgagacagcggtagtatagctttttaggctgtataagaatttttgaaaatctcgagcaaatttcttgtaaacgctcacaggagatgatatactgttctagtaaattataaattaaggtaggactattctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1126:SSA_1127|SSA_1126:SSA_1127:Thiamine biosynthesis lipoprotein, putative:H2O-forming NADH dehydrogenase, putative:<-->:1151613..1151870 258 attatcacaacctttctaaaattaacctctctaaccttattatatcaaaaagataccggtttcacaatcttaaaattgttatattttcagaaaattaactttcgcacaaagctgtattttcgaagcgatgagacagcggtagtatagctttttaggctgtataagaatttttgaaaatctcgagcaaatttcttgtaaacgctcacaggagatgatatactgttctagtaaattataaattaaggtaggactattctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attatcacaacctttctaaaattaacctctctaaccttattatatcaaaaagataccggtttcacaatcttaaaattgttatattttcagaaaattaactttcgcacaaagctgtattttcgaagcgatgagacagcggtagtatagctttttaggctgtataagaatttttgaaaatctcgagcaaatttcttgtaaacgctcacaggagatgatatactgttctagtaaattataaattaaggtaggactattctt Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 1 End: 144 M I T T F L K L T S L T L L Y Q K D T G F T I L K L L Y F Q K I N F R T K L Y F R S D E T A V V .................................................................................................................. Protein_Len: 43 Strand: - Start: 90 End: 218 ......................................................................................... F I L K R V F S Y K R L S S V A T T Y S K L S Y L F K Q F D R A F K K Y V S V P S S M ........................................ Protein_Len: 53 Strand: - Start: 82 End: 240 ................................................................................. I K L F N V K A C L Q I K S A I L C R Y Y L K K P Q I L I K S F R S C I E Q L R E C S I I Y Q E L L N Y M .................. attatcacaacctttctaaaattaacctctctaaccttattatatcaaaaagataccggtttcacaatcttaaaattgttatattttcagaaaattaactttcgcacaaagctgtattttcgaagcgatgagacagcggtagtatagctttttaggctgtataagaatttttgaaaatctcgagcaaatttcttgtaaacgctcacaggagatgatatactgttctagtaaattataaattaaggtaggactattctt 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: 87 Start: 39 End: 68 ......................................ATTGTGAAACCGGTATCTTTTTGATATAAT.............................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attatcacaacctttctaaaattaacctctctaaccttattatatcaaaaagataccggtttcacaatcttaaaattgttatattttcagaaaattaactttcgcacaaagctgtattttcgaagcgatgagacagcggtagtatagctttttaggctgtataagaatttttgaaaatctcgagcaaatttcttgtaaacgctcacaggagatgatatactgttctagtaaattataaattaaggtaggactattctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1126:SSA_1127|SSA_1126:SSA_1127:Thiamine biosynthesis lipoprotein, putative:H2O-forming NADH dehydrogenase, putative:<-->:1151613..1151870 258 attatcacaacctttctaaaattaacctctctaaccttattatatcaaaaagataccggtttcacaatcttaaaattgttatattttcagaaaattaactttcgcacaaagctgtattttcgaagcgatgagacagcggtagtatagctttttaggctgtataagaatttttgaaaatctcgagcaaatttcttgtaaacgctcacaggagatgatatactgttctagtaaattataaattaaggtaggactattctt Intra-Species Hit: Count: 1 Min: 1 Max: 258 Len: 258 Subject: NC_009009_SSA_1126_SSA_1127|Thiamine biosynthesis lipoprotein, putative:H2O-forming NADH dehydrogenase, putative|NEGATIVE:POSITIVE|[1151613,1151870]|258 HSP 1 e-value: 1.0E-144 bit: 511.0 Len: 258 Query Start:1 Query End:258 Subject Strand: POSITIVE Subject Start: 1 Subject End: 258 attatcacaacctttctaaaattaacctctctaaccttattatatcaaaaagataccggtttcacaatcttaaaattgttatattttcagaaaattaactttcgcacaaagctgtattttcgaagcgatgagacagcggtagtatagctttttaggctgtataagaatttttgaaaatctcgagcaaatttcttgtaaacgctcacaggagatgatatactgttctagtaaattataaattaaggtaggactattctt attatcacaacctttctaaaattaacctctctaaccttattatatcaaaaagataccggtttcacaatcttaaaattgttatattttcagaaaattaactttcgcacaaagctgtattttcgaagcgatgagacagcggtagtatagctttttaggctgtataagaatttttgaaaatctcgagcaaatttcttgtaaacgctcacaggagatgatatactgttctagtaaattataaattaaggtaggactattctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUCACAACCUUUCUAAAAUUAACCUCUCUAACCUUAUUAUAUCAAAAAGAUACCGGUUUCACAAUCUUAAAAUUGUUAUAUUUUCAGAAAAUUAACUUUCGCACAAAGCUGUAUUUUCGAAGCGAUGAGACAGCGGUAGUAUAGCUUUUUAGGCUGUAUAAGAAUUUUUGAAAAUCUCGAGCAAAUUUCUUGUAAACGCUCACAGGAGAUGAUAUACUGUUCUAGUAAAUUAUAAAUUAAGGUAGGACUAUUCUU .............................(((.(((((((((((......(((...((((.((............(((((..(((((((((((.................(((((....(((...)))....)))))....((((((((.....)))))))).....)))))))))))....))))).((((((((........)))))))).))...)))).))).......)))))..)))))).)))........ (-48.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAUAGUCCUACCUUAAUUUAUAAUUUACUAGAACAGUAUAUCAUCUCCUGUGAGCGUUUACAAGAAAUUUGCUCGAGAUUUUCAAAAAUUCUUAUACAGCCUAAAAAGCUAUACUACCGCUGUCUCAUCGCUUCGAAAAUACAGCUUUGUGCGAAAGUUAAUUUUCUGAAAAUAUAACAAUUUUAAGAUUGUGAAACCGGUAUCUUUUUGAUAUAAUAAGGUUAGAGAGGUUAAUUUUAGAAAGGUUGUGAUAAU ((((((......................((((.....))))....(((((....(((((.............))))))))))........)))))).((((((((................(((((....(((...)))....)))))........(((((((((((((((........((((((....))))))...(((.(((((.....))))).....))))))))).)))))))))....))))))))..... (-46.02) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 876 140 91 231 182 NC_009009:SSA_1126|5end_Thiamine_biosynthesis_lipoprotein,_putative_1151522..1151752_NEGATIVE 378 149 102 169 127 NC_009009:SSA_0743|5end_Transcriptional_repressor_(arginine_synthesis),_putative_725759..725989_NEGATIVE 340 148 103 94 53 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 316 158 112 61 10 NC_009009:SSA_0725|5end_hypothetical_protein_710247..710477_POSITIVE 308 160 111 222 174 NC_009009:SSA_0696|5end_hypothetical_protein_679154..679384_POSITIVE 306 160 111 221 154 NC_009009:SSA_2196|5end_Conserved_uncharacterized_protein_2197330..2197560_NEGATIVE 306 156 111 171 121 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 304 69 27 126 93 NC_009009:SSA_0996|5end_cGMP-specific_phosphodiesterase,_putative_996282..996512_POSITIVE 302 148 101 222 171 NC_009009:SSA_1009|5end_Galactose-1-phosphate-uridylyltransferase,_putative_1011254..1011484_POSITIVE 294 65 27 138 101 NC_009009:SSA_1818|5end_Very_short_patch_repair_endonuclease,_putative_1806110..1806340_NEGATIVE 291 167 124 139 95 NC_009009:SSA_0364|5end_Serine/threonine:Na+_symporter,_putative_356348..356578_NEGATIVE 289 121 87 201 156 NC_009009:SSA_1269|5end_hypothetical_protein_1293352..1293582_NEGATIVE 286 148 101 73 20 NC_009009:SSA_0892|5end_ATP-binding_cassette_lipoprotein,_putative_884226..884456_POSITIVE 284 143 103 195 137 NC_009009:SSA_0370|5end_Acetyltransferase,_GNAT_family,_putative_360382..360612_NEGATIVE 275 162 122 155 106 NC_009009:SSA_2373|5end_DNA_replication_and_repair_protein_recF,_putative_2374208..2374438_POSITIVE 271 139 93 185 137 NC_009009:SSA_2219|5end_UDP-glucose_4-epimerase,_putative_2220827..2221057_NEGATIVE 269 146 104 227 184 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 269 160 111 184 132 NC_009009:SSA_0871|5end_Cell_division_protein_FtsX,_putative_863621..863851_POSITIVE 267 150 104 75 17 NC_009009:SSA_0406|5end_hypothetical_protein_402918..403148_NEGATIVE 264 139 97 66 7 NC_009009:SSA_2165|5end_ABC-type_oligopeptide_transporter,_periplasmic_component,_putative_2161734..2161964_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 148 102 151 110 NC_009009:SSA_0744|3end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_725776..725926_NEGATIVE 304 69 27 96 63 NC_009009:SSA_0995|3end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_996332..996482_POSITIVE 294 65 27 53 16 NC_009009:SSA_1819|3end_Valyl-tRNA_synthetase,_putative_1806195..1806345_NEGATIVE 292 171 131 117 77 NC_009009:SSA_1548|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_1551119..1551269_NEGATIVE 290 158 121 46 8 NC_009009:SSA_0724|3end_ABC-type_multidrug/protein/lipid_transport_system_(pediocin_PA-1_exporter),_ATPase_and_permease_components,_putative_710312..710462_POSITIVE 289 121 87 77 32 NC_009009:SSA_1270|3end_Flavodoxin_1293476..1293626_NEGATIVE 284 149 110 74 27 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 267 150 104 82 24 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 262 161 122 151 103 NC_009009:SSA_2372|3end_hypothetical_protein_2374285..2374435_POSITIVE 262 165 124 59 24 NC_009009:SSA_1368|3end_hypothetical_protein_1383748..1383898_NEGATIVE 261 150 106 75 24 NC_009009:SSA_2027|3end_P-type_ATPase-metal/cation_transport_(probably_copper),_putative_2033109..2033259_NEGATIVE 260 162 121 68 27 NC_009009:SSA_0461|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_464905..465055_POSITIVE 255 162 123 122 77 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 250 148 103 150 106 NC_009009:SSA_0371|3end_NADP-specific_glutamate_dehydrogenase,_putative_360413..360563_NEGATIVE 249 228 187 150 104 NC_009009:SSA_0750|3end_hypothetical_protein_732255..732405_POSITIVE 247 165 121 64 22 NC_009009:SSA_1239|3end_hypothetical_protein_1263151..1263301_NEGATIVE 244 159 111 151 106 NC_009009:SSA_1543|3end_hypothetical_protein_1548217..1548367_POSITIVE 242 158 111 148 104 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE 239 150 101 70 10 NC_009009:SSA_0830|3end_Glycosyltransferase,_putative_815734..815884_POSITIVE 239 148 102 146 111 NC_009009:SSA_0355|3end_DNA_mismatch_repair_protein,_putative_349260..349410_POSITIVE