Origin IGS: gcaataaaagaacgagcgagcagtgttgaagagctcacagttttacttattcttgataaaataacaaaaaggaagaatccaaagtaactttgcagtgaaagcggattcttcttttttgcttggaaatttgtgggaatgcggcagcagatagctttgtgagttttctaaaaacatataggcttgaatattttactcatctgtcatcggtttactatttactttttatacgctttttggtataatagttcatgttataaaatgtaacatcaaaggaggttctatcc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggatagaacctcctttgatgttacattttataacatgaactattataccaaaaagcgtataaaaagtaaatagtaaaccgatgacagatgagtaaaatattcaagcctatatgtttttagaaaactcacaaagctatctgctgccgcattcccacaaatttccaagcaaaaaagaagaatccgctttcactgcaaagttactttggattcttcctttttgttattttatcaagaataagtaaaactgtgagctcttcaacactgctcgctcgttcttttattgc Mask Tandem Repeat Region ================================================ gcaataaaagaacgagcgagcagtgttgaagagctcacagttttacttattcttgataaaataacaaaaaggaagaatccaaagtaactttgcagtgaaagcggattcttcttttttgcttggaaatttgtgggaatgcggcagcagatagctttgtgagttttctaaaaacatataggcttgaatattttactcatctgtcatcggtttactatttactttttatacgctttttggtataatagttcatgttataaaatgtaacatcaaaggaggttctatcc Find is-nt database================================================ Query_seq: SSA_1065:SSA_1066|SSA_1065:SSA_1066:Beta-hexosamidase A, putative:ABC-type oligopeptide transport system, putative:->->:1084191..1084474 284 gcaataaaagaacgagcgagcagtgttgaagagctcacagttttacttattcttgataaaataacaaaaaggaagaatccaaagtaactttgcagtgaaagcggattcttcttttttgcttggaaatttgtgggaatgcggcagcagatagctttgtgagttttctaaaaacatataggcttgaatattttactcatctgtcatcggtttactatttactttttatacgctttttggtataatagttcatgttataaaatgtaacatcaaaggaggttctatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1065:SSA_1066|SSA_1065:SSA_1066:Beta-hexosamidase A, putative:ABC-type oligopeptide transport system, putative:->->:1084191..1084474 284 gcaataaaagaacgagcgagcagtgttgaagagctcacagttttacttattcttgataaaataacaaaaaggaagaatccaaagtaactttgcagtgaaagcggattcttcttttttgcttggaaatttgtgggaatgcggcagcagatagctttgtgagttttctaaaaacatataggcttgaatattttactcatctgtcatcggtttactatttactttttatacgctttttggtataatagttcatgttataaaatgtaacatcaaaggaggttctatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1065:SSA_1066|SSA_1065:SSA_1066:Beta-hexosamidase A, putative:ABC-type oligopeptide transport system, putative:->->:1084191..1084474 284 gcaataaaagaacgagcgagcagtgttgaagagctcacagttttacttattcttgataaaataacaaaaaggaagaatccaaagtaactttgcagtgaaagcggattcttcttttttgcttggaaatttgtgggaatgcggcagcagatagctttgtgagttttctaaaaacatataggcttgaatattttactcatctgtcatcggtttactatttactttttatacgctttttggtataatagttcatgttataaaatgtaacatcaaaggaggttctatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaataaaagaacgagcgagcagtgttgaagagctcacagttttacttattcttgataaaataacaaaaaggaagaatccaaagtaactttgcagtgaaagcggattcttcttttttgcttggaaatttgtgggaatgcggcagcagatagctttgtgagttttctaaaaacatataggcttgaatattttactcatctgtcatcggtttactatttactttttatacgctttttggtataatagttcatgttataaaatgtaacatcaaaggaggttctatcc Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 105 End: 239 ........................................................................................................ M L L F C L E I C G N A A A D S F V S F L K T Y R L E Y F T H L S S V Y Y L L F I R F L V ............................................. Protein_Len: 33 Strand: + Start: 185 End: 283 ........................................................................................................................................................................................ M F Y S S V I G L L F T F Y T L F G I I V H V I K C N I K G G S I . Protein_Len: 47 Strand: - Start: 46 End: 186 ............................................. K N K I F Y C F P L I W L L K A T F A S E E K K S P F K H S H P L L Y S Q S N E L F M Y A Q M .................................................................................................. Protein_Len: 49 Strand: - Start: 3 End: 149 .. I F S R A L L T S S S V T K S I R S L I V F L F F G F Y S Q L S L P N K K K A Q F N T P I R C C M ....................................................................................................................................... gcaataaaagaacgagcgagcagtgttgaagagctcacagttttacttattcttgataaaataacaaaaaggaagaatccaaagtaactttgcagtgaaagcggattcttcttttttgcttggaaatttgtgggaatgcggcagcagatagctttgtgagttttctaaaaacatataggcttgaatattttactcatctgtcatcggtttactatttactttttatacgctttttggtataatagttcatgttataaaatgtaacatcaaaggaggttctatcc 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: 89 Start: 214 End: 243 .....................................................................................................................................................................................................................ATTTACTTTTTATACGCTTTTTGGTATAAT......................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 33 End: 62 ................................GCTCACAGTTTTACTTATTCTTGATAAAAT.............................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcaataaaagaacgagcgagcagtgttgaagagctcacagttttacttattcttgataaaataacaaaaaggaagaatccaaagtaactttgcagtgaaagcggattcttcttttttgcttggaaatttgtgggaatgcggcagcagatagctttgtgagttttctaaaaacatataggcttgaatattttactcatctgtcatcggtttactatttactttttatacgctttttggtataatagttcatgttataaaatgtaacatcaaaggaggttctatcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1065:SSA_1066|SSA_1065:SSA_1066:Beta-hexosamidase A, putative:ABC-type oligopeptide transport system, putative:->->:1084191..1084474 284 gcaataaaagaacgagcgagcagtgttgaagagctcacagttttacttattcttgataaaataacaaaaaggaagaatccaaagtaactttgcagtgaaagcggattcttcttttttgcttggaaatttgtgggaatgcggcagcagatagctttgtgagttttctaaaaacatataggcttgaatattttactcatctgtcatcggtttactatttactttttatacgctttttggtataatagttcatgttataaaatgtaacatcaaaggaggttctatcc Intra-Species Hit: Count: 1 Min: 1 Max: 284 Len: 284 Subject: NC_009009_SSA_1065_SSA_1066|Beta-hexosamidase A, putative:ABC-type oligopeptide transport system, putative|POSITIVE:POSITIVE|[1084191,1084474]|284 HSP 1 e-value: 1.0E-159 bit: 563.0 Len: 284 Query Start:1 Query End:284 Subject Strand: POSITIVE Subject Start: 1 Subject End: 284 gcaataaaagaacgagcgagcagtgttgaagagctcacagttttacttattcttgataaaataacaaaaaggaagaatccaaagtaactttgcagtgaaagcggattcttcttttttgcttggaaatttgtgggaatgcggcagcagatagctttgtgagttttctaaaaacatataggcttgaatattttactcatctgtcatcggtttactatttactttttatacgctttttggtataatagttcatgttataaaatgtaacatcaaaggaggttctatcc gcaataaaagaacgagcgagcagtgttgaagagctcacagttttacttattcttgataaaataacaaaaaggaagaatccaaagtaactttgcagtgaaagcggattcttcttttttgcttggaaatttgtgggaatgcggcagcagatagctttgtgagttttctaaaaacatataggcttgaatattttactcatctgtcatcggtttactatttactttttatacgctttttggtataatagttcatgttataaaatgtaacatcaaaggaggttctatcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAUAAAAGAACGAGCGAGCAGUGUUGAAGAGCUCACAGUUUUACUUAUUCUUGAUAAAAUAACAAAAAGGAAGAAUCCAAAGUAACUUUGCAGUGAAAGCGGAUUCUUCUUUUUUGCUUGGAAAUUUGUGGGAAUGCGGCAGCAGAUAGCUUUGUGAGUUUUCUAAAAACAUAUAGGCUUGAAUAUUUUACUCAUCUGUCAUCGGUUUACUAUUUACUUUUUAUACGCUUUUUGGUAUAAUAGUUCAUGUUAUAAAAUGUAACAUCAAAGGAGGUUCUAUCC ........(((((...(((((.(((((..(((((((((((.....(.(((((((.(((((.(((((((((((((((((((...(((....))).((....)))))))))))))))))).)))....)))))))))))).)..(((.....)))))))))))))).....)))))....))))).........(((......................(((..((((((........)))))).)))..(((((((.....))))))).....)))))))).... (-65.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUAGAACCUCCUUUGAUGUUACAUUUUAUAACAUGAACUAUUAUACCAAAAAGCGUAUAAAAAGUAAAUAGUAAACCGAUGACAGAUGAGUAAAAUAUUCAAGCCUAUAUGUUUUUAGAAAACUCACAAAGCUAUCUGCUGCCGCAUUCCCACAAAUUUCCAAGCAAAAAAGAAGAAUCCGCUUUCACUGCAAAGUUACUUUGGAUUCUUCCUUUUUGUUAUUUUAUCAAGAAUAAGUAAAACUGUGAGCUCUUCAACACUGCUCGCUCGUUCUUUUAUUGC .(((((((......((.((((((.......)))))).))...............(((.......((((.(((((..............((((((...))))))...(((........)))............))))).))))..))).................((((((((.((((((((((.....(((....))).....)))))))))).)))))))).)))))))...((((((..((...((((((...........))))))...))..)))))).. (-52.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 166 121 185 137 NC_009009:SSA_0115|5end_50S_ribosomal_protein_L29,_putative_112402..112632_POSITIVE 342 130 83 61 5 NC_009009:SSA_0380|5end_Enzyme_of_poly-gamma-glutamate_biosynthesis_(capsule_formation),_putative_370916..371146_POSITIVE 336 154 111 209 164 NC_009009:SSA_1872|5end_Cell_division_protein,_putative_1869186..1869416_NEGATIVE 332 60 16 211 157 NC_009009:SSA_1563|5end_Metal-dependent_hydrolase,_beta-lactamase_superfamily_I,_putative_1567256..1567486_NEGATIVE 324 57 12 203 157 NC_009009:SSA_2132|5end_Ure_cluster_protein,_putative_2134170..2134400_POSITIVE 317 140 92 177 131 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 317 147 102 137 89 NC_009009:SSA_0498|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_systems,_permease_components,_putative_497910..498140_POSITIVE 310 130 83 215 159 NC_009009:SSA_0939|5end_Inositol_monophosphatase_(Mg++_dependent),_putative_946810..947040_POSITIVE 288 159 118 159 102 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 285 140 92 74 36 NC_009009:SSA_0387|5end_Transcriptional_regulator,_GntR_family,_putative_382343..382573_NEGATIVE 285 145 101 40 1 NC_009009:SSA_0323|5end_Flavoprotein,_putative_316799..317029_NEGATIVE 283 122 88 169 137 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 281 149 102 60 16 NC_009009:SSA_0370|5end_Acetyltransferase,_GNAT_family,_putative_360382..360612_NEGATIVE 279 213 176 97 58 NC_009009:SSA_1099|5end_Calcium_binding_hemolysin-like_protein,_putative_1115361..1115591_POSITIVE 275 154 118 188 158 NC_009009:SSA_1302|5end_tRNA_(Guanine-N(1)-)-methyltransferase,_putative_1322484..1322714_NEGATIVE 275 142 101 194 148 NC_009009:SSA_0578|5end_Nicotinate-nucleotide_adenylyltransferase,_putative_571591..571821_POSITIVE 271 138 92 74 24 NC_009009:SSA_1400|5end_Pyridoxal_kinase,_putative_1413072..1413302_NEGATIVE 270 137 91 185 142 NC_009009:SSA_1514|5end_Cell-wall_biogenesis_glycosyltransferase,_putative_1521780..1522010_NEGATIVE 269 40 2 69 34 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 269 157 111 62 13 NC_009009:SSA_1441|5end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1445183..1445413_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 147 102 144 96 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 305 157 120 146 109 NC_009009:SSA_2056|3end_Cinnamoyl_ester_hydrolase,_putative_2059593..2059743_POSITIVE 301 152 111 145 96 NC_009009:SSA_0592|3end_hypothetical_protein_584248..584398_POSITIVE 287 118 78 83 47 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 286 152 116 59 23 NC_009009:SSA_1212|3end_Ribose-phosphate_pyrophosphokinase_2,_putative_1236437..1236587_POSITIVE 283 122 88 74 42 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 277 166 129 148 110 NC_009009:SSA_2267|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2267190..2267340_POSITIVE 272 120 73 148 86 NC_009009:SSA_0616|3end_YlbN-like_protein,_putative_609855..610005_POSITIVE 269 56 14 139 107 NC_009009:SSA_1476|3end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1482448..1482598_POSITIVE 269 157 111 62 13 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 266 239 192 128 89 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 264 166 131 133 98 NC_009009:SSA_1480|3end_hypothetical_protein_1483960..1484110_NEGATIVE 263 159 119 40 2 NC_009009:SSA_2034|3end_50S_ribosomal_protein_L13,_putative_2038798..2038948_NEGATIVE 262 148 102 147 106 NC_009009:SSA_0152|3end_hypothetical_protein_148731..148881_POSITIVE 259 150 101 142 102 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 258 160 115 45 5 NC_009009:SSA_2380|3end_hypothetical_protein_2385665..2385815_NEGATIVE 258 55 22 75 41 NC_009009:SSA_1343|3end_Aspartate_carbamoyltransferase,_putative_1361042..1361192_NEGATIVE 257 154 118 151 112 NC_009009:SSA_2170|3end_hypothetical_protein_2169557..2169707_NEGATIVE 255 170 126 85 28 NC_009009:SSA_2275|3end_hypothetical_protein_2275225..2275375_NEGATIVE 255 57 13 101 58 NC_009009:SSA_2016|3end_Phosphoglycerate_mutase,_putative_2015592..2015742_NEGATIVE