Origin IGS: tcttttgtcctccgaatcatattatttcttattactatagtaaacgttttctgccgaaaaatcaacatttaacagtaaaaaaatattttttctgcaaaacgcttgacatatttttgatcatggtaaaatgatattcgtaaaggcgataaaatcgctttcaaaagttaaaaatatttataaggagatttttgcaa .........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 ttgcaaaaatctccttataaatatttttaacttttgaaagcgattttatcgcctttacgaatatcattttaccatgatcaaaaatatgtcaagcgttttgcagaaaaaatatttttttactgttaaatgttgatttttcggcagaaaacgtttactatagtaataagaaataatatgattcggaggacaaaaga Mask Tandem Repeat Region ================================================ tcttttgtcctccgaatcatattatttcttattactatagtaaacgttttctgccgaaaaatcaacatttaacagtaaaaaaatattttttctgcaaaacgcttgacatatttttgatcatggtaaaatgatattcgtaaaggcgataaaatcgctttcaaaagttaaaaatatttataaggagatttttgcaa Find is-nt database================================================ Query_seq: SSA_0455:SSA_0456|SSA_0455:SSA_0456:Sucrose-6-phosphate hydrolase, putative:Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific, putative:<-->:458541..458734 194 tcttttgtcctccgaatcatattatttcttattactatagtaaacgttttctgccgaaaaatcaacatttaacagtaaaaaaatattttttctgcaaaacgcttgacatatttttgatcatggtaaaatgatattcgtaaaggcgataaaatcgctttcaaaagttaaaaatatttataaggagatttttgcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0455:SSA_0456|SSA_0455:SSA_0456:Sucrose-6-phosphate hydrolase, putative:Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific, putative:<-->:458541..458734 194 tcttttgtcctccgaatcatattatttcttattactatagtaaacgttttctgccgaaaaatcaacatttaacagtaaaaaaatattttttctgcaaaacgcttgacatatttttgatcatggtaaaatgatattcgtaaaggcgataaaatcgctttcaaaagttaaaaatatttataaggagatttttgcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0455:SSA_0456|SSA_0455:SSA_0456:Sucrose-6-phosphate hydrolase, putative:Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific, putative:<-->:458541..458734 194 tcttttgtcctccgaatcatattatttcttattactatagtaaacgttttctgccgaaaaatcaacatttaacagtaaaaaaatattttttctgcaaaacgcttgacatatttttgatcatggtaaaatgatattcgtaaaggcgataaaatcgctttcaaaagttaaaaatatttataaggagatttttgcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttttgtcctccgaatcatattatttcttattactatagtaaacgttttctgccgaaaaatcaacatttaacagtaaaaaaatattttttctgcaaaacgcttgacatatttttgatcatggtaaaatgatattcgtaaaggcgataaaatcgctttcaaaagttaaaaatatttataaggagatttttgcaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 21 End: 128 .................... M I S Y Y Y S K R F L P K N Q H L T V K K Y F F C K T L D I F L I M V K .................................................................. Protein_Len: 30 Strand: - Start: 72 End: 161 ....................................................................... C Y F F I K E A F R K V Y K Q D H Y F S I R L P S L I A K M ................................. tcttttgtcctccgaatcatattatttcttattactatagtaaacgttttctgccgaaaaatcaacatttaacagtaaaaaaatattttttctgcaaaacgcttgacatatttttgatcatggtaaaatgatattcgtaaaggcgataaaatcgctttcaaaagttaaaaatatttataaggagatttttgcaa 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: 81 Start: 37 End: 66 ....................................GTTGATTTTTCGGCAGAAAACGTTTACTAT................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcttttgtcctccgaatcatattatttcttattactatagtaaacgttttctgccgaaaaatcaacatttaacagtaaaaaaatattttttctgcaaaacgcttgacatatttttgatcatggtaaaatgatattcgtaaaggcgataaaatcgctttcaaaagttaaaaatatttataaggagatttttgcaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -7.7 Tail_Score: -3.57561 Start: 143 End: 155 Full_Region: ATGATATTCGTAAAG GCGAT AAA ATCGC TTTCAAAAGTTAAAA ..............................................................................................................................................GCGATAAAATCGC....................................... Find igs database================================================ Query_seq: SSA_0455:SSA_0456|SSA_0455:SSA_0456:Sucrose-6-phosphate hydrolase, putative:Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific, putative:<-->:458541..458734 194 tcttttgtcctccgaatcatattatttcttattactatagtaaacgttttctgccgaaaaatcaacatttaacagtaaaaaaatattttttctgcaaaacgcttgacatatttttgatcatggtaaaatgatattcgtaaaggcgataaaatcgctttcaaaagttaaaaatatttataaggagatttttgcaa Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: NC_009009_SSA_0455_SSA_0456|Sucrose-6-phosphate hydrolase, putative:Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific, putative|NEGATIVE:POSITIVE|[458541,458734]|194 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 tcttttgtcctccgaatcatattatttcttattactatagtaaacgttttctgccgaaaaatcaacatttaacagtnnnnnnntattttttctgcaaaacgcttgacatatttttgatcatggtaaaatgatattcgtaaaggcgataaaatcgctttcaaaagttaaaaatatttataaggagatttttgcaa tcttttgtcctccgaatcatattatttcttattactatagtaaacgttttctgccgaaaaatcaacatttaacagtaaaaaaatattttttctgcaaaacgcttgacatatttttgatcatggtaaaatgatattcgtaaaggcgataaaatcgctttcaaaagttaaaaatatttataaggagatttttgcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUUGUCCUCCGAAUCAUAUUAUUUCUUAUUACUAUAGUAAACGUUUUCUGCCGAAAAAUCAACAUUUAACAGUAAAAAAAUAUUUUUUCUGCAAAACGCUUGACAUAUUUUUGAUCAUGGUAAAAUGAUAUUCGUAAAGGCGAUAAAAUCGCUUUCAAAAGUUAAAAAUAUUUAUAAGGAGAUUUUUGCAA .........((((...(((............((((....)))).(((((..(((.((((((......((((....)))).......)))))).))))))))..))).((((((((((((((......))).........((((((((...)))))))).....)))))))))))......)))).......... (-28.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCAAAAAUCUCCUUAUAAAUAUUUUUAACUUUUGAAAGCGAUUUUAUCGCCUUUACGAAUAUCAUUUUACCAUGAUCAAAAAUAUGUCAAGCGUUUUGCAGAAAAAAUAUUUUUUUACUGUUAAAUGUUGAUUUUUCGGCAGAAAACGUUUACUAUAGUAAUAAGAAAUAAUAUGAUUCGGAGGACAAAAGA .........((((((((((..(((((((.(((...(.(((((.((((...(((.........(((((......))))).........(((((.(((((.((((.(((((....))))).)))).)))))))))).....)))..))))))))).)...)))....))))))).)))))...)))))........ (-33.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 763 140 91 231 182 NC_009009:SSA_0455|5end_Sucrose-6-phosphate_hydrolase,_putative_458450..458680_NEGATIVE 266 169 133 67 29 NC_009009:SSA_2031|5end_Conserved_domain_uncharacterized_protein_2037153..2037383_POSITIVE 252 160 112 174 123 NC_009009:SSA_1199|5end_Phosphinothricin_acetyltransferase,_putative_1223958..1224188_NEGATIVE 251 81 41 51 11 NC_009009:SSA_2381|5end_DegP_protein,_putative_2386298..2386528_POSITIVE 246 124 91 192 159 NC_009009:SSA_1069|5end_Lipoprotein_signal_peptidase,_putative_1088291..1088521_POSITIVE 241 54 13 188 147 NC_009009:SSA_2392|5end_50S_ribosomal_protein_L36,_putative_120198..120428_POSITIVE 239 50 8 141 96 NC_009009:SSA_2130|5end_hypothetical_protein_2133464..2133694_POSITIVE 238 50 7 132 98 NC_009009:SSA_2068|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_2071311..2071541_NEGATIVE 224 156 111 145 109 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 213 145 108 186 134 NC_009009:SSA_1269|5end_hypothetical_protein_1293352..1293582_NEGATIVE 211 130 91 219 180 NC_009009:SSA_0601|5end_Phosphorylase,_Pnp/Udp_family,_putative_589147..589377_POSITIVE 208 155 119 220 179 NC_009009:SSA_0431|5end_hypothetical_protein_433275..433505_NEGATIVE 206 130 93 71 38 NC_009009:SSA_0309|5end_Glyoxalase/Bleomycin_resistance_protein/dioxygenase_domain,_putative_304894..305124_POSITIVE 205 115 86 98 64 NC_009009:SSA_0030|5end_Phosphoribosylformylglycinamidine_synthase,_putative_32610..32840_POSITIVE 202 162 136 50 25 NC_009009:SSA_0962|5end_Lactoylglutathione_lyase,_putative_970965..971195_POSITIVE 201 144 113 231 200 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 201 144 113 97 66 NC_009009:SSA_1552|5end_hypothetical_protein_1554913..1555143_POSITIVE 199 183 141 226 180 NC_009009:SSA_2093|5end_PTS_system,_membrane_component,_putative_2097462..2097692_NEGATIVE 199 77 35 162 127 NC_009009:SSA_1607|5end_Formamidopyrimidine-DNA_glycosylase,_putative_1613255..1613485_NEGATIVE 195 135 91 46 3 NC_009009:SSA_1995|5end_hypothetical_protein_1993358..1993588_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 47 3 63 4 NC_009009:SSA_0042|3end_Amino_acid_recemase,_putative_48671..48821_POSITIVE 241 55 19 115 79 NC_009009:SSA_0323|3end_Flavoprotein,_putative_315624..315774_NEGATIVE 238 50 7 41 7 NC_009009:SSA_2069|3end_Prolyl-tRNA_synthetase,_putative_2071402..2071552_NEGATIVE 224 156 111 143 107 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 215 158 115 85 43 NC_009009:SSA_1739|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1727065..1727215_POSITIVE 213 145 108 62 10 NC_009009:SSA_1270|3end_Flavodoxin_1293476..1293626_NEGATIVE 209 157 121 83 52 NC_009009:SSA_2324|3end_hypothetical_protein_2328847..2328997_NEGATIVE 205 115 86 78 44 NC_009009:SSA_0028|3end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_32670..32820_POSITIVE 199 77 35 134 99 NC_009009:SSA_1608|3end_hypothetical_protein_1613283..1613433_NEGATIVE 196 159 117 124 90 NC_009009:SSA_1793|3end_Histidine_kinase_(sensor_protein),_putative_1775126..1775276_NEGATIVE 195 57 15 130 93 NC_009009:SSA_1565|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1568608..1568758_NEGATIVE 194 124 82 141 101 NC_009009:SSA_1736|3end_L-cysteine_desulfhydrase,_putative_1721453..1721603_NEGATIVE 193 30 1 123 99 NC_009009:SSA_2247|3end_hypothetical_protein_2243135..2243285_POSITIVE 191 126 88 84 43 NC_009009:SSA_1446|3end_Histidinol_dehydrogenase,_putative_1447898..1448048_NEGATIVE 191 41 4 150 111 NC_009009:SSA_0129|3end_Translation_initiation_factor_IF-1,_putative_120255..120405_POSITIVE 189 189 141 65 24 NC_009009:SSA_0290|3end_hypothetical_protein_284084..284234_NEGATIVE 186 32 2 87 63 NC_009009:SSA_1207|3end_Phosphate_acetyltransferase,_putative_1231297..1231447_NEGATIVE 185 77 44 88 48 NC_009009:SSA_0928|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938525..938675_POSITIVE 185 147 101 150 108 NC_009009:SSA_0447|3end_Magnesium_and_cobalt_transporter,_putative_445457..445607_NEGATIVE 184 138 98 36 1 NC_009009:SSA_0811|3end_hypothetical_protein_793526..793676_POSITIVE