Origin IGS: gatgagattgggagttattcccagtcttttttgttggaaaatcattggataaagtactcacttcacttgtagctatagagcctgcctatggcatttcctatgtagaaaatatgcaggcagcgttcagcagaccgcctttttatgatacaatggtaagatgaagtcagtagacatctgctggctgtttcatcaggaagagagggataagagagcaagcct .........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 aggcttgctctcttatccctctcttcctgatgaaacagccagcagatgtctactgacttcatcttaccattgtatcataaaaaggcggtctgctgaacgctgcctgcatattttctacataggaaatgccataggcaggctctatagctacaagtgaagtgagtactttatccaatgattttccaacaaaaaagactgggaataactcccaatctcatc Mask Tandem Repeat Region ================================================ gatgagattgggagttattcccagtcttttttgttggaaaatcattggataaagtactcacttcacttgtagctatagagcctgcctatggcatttcctatgtagaaaatatgcaggcagcgttcagcagaccgcctttttatgatacaatggtaagatgaagtcagtagacatctgctggctgtttcatcaggaagagagggataagagagcaagcct Find is-nt database================================================ Query_seq: SSA_0599:SSA_0601|SSA_0599:SSA_0601:hypothetical protein:Phosphorylase, Pnp/Udp family, putative:->->:589068..589286 219 gatgagattgggagttattcccagtcttttttgttggaaaatcattggataaagtactcacttcacttgtagctatagagcctgcctatggcatttcctatgtagaaaatatgcaggcagcgttcagcagaccgcctttttatgatacaatggtaagatgaagtcagtagacatctgctggctgtttcatcaggaagagagggataagagagcaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0599:SSA_0601|SSA_0599:SSA_0601:hypothetical protein:Phosphorylase, Pnp/Udp family, putative:->->:589068..589286 219 gatgagattgggagttattcccagtcttttttgttggaaaatcattggataaagtactcacttcacttgtagctatagagcctgcctatggcatttcctatgtagaaaatatgcaggcagcgttcagcagaccgcctttttatgatacaatggtaagatgaagtcagtagacatctgctggctgtttcatcaggaagagagggataagagagcaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0599:SSA_0601|SSA_0599:SSA_0601:hypothetical protein:Phosphorylase, Pnp/Udp family, putative:->->:589068..589286 219 gatgagattgggagttattcccagtcttttttgttggaaaatcattggataaagtactcacttcacttgtagctatagagcctgcctatggcatttcctatgtagaaaatatgcaggcagcgttcagcagaccgcctttttatgatacaatggtaagatgaagtcagtagacatctgctggctgtttcatcaggaagagagggataagagagcaagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgagattgggagttattcccagtcttttttgttggaaaatcattggataaagtactcacttcacttgtagctatagagcctgcctatggcatttcctatgtagaaaatatgcaggcagcgttcagcagaccgcctttttatgatacaatggtaagatgaagtcagtagacatctgctggctgtttcatcaggaagagagggataagagagcaagcct Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 45 End: 158 ............................................ M D K V L T S L V A I E P A Y G I S Y V E N M Q A A F S R P P F Y D T M V R ............................................................. Protein_Len: 50 Strand: - Start: 66 End: 215 ................................................................. K Y S Y L R G I A N G I Y F I H L C R E A S R R K I I C H Y S S T L L C R S A T E D P L S P Y S L M .... gatgagattgggagttattcccagtcttttttgttggaaaatcattggataaagtactcacttcacttgtagctatagagcctgcctatggcatttcctatgtagaaaatatgcaggcagcgttcagcagaccgcctttttatgatacaatggtaagatgaagtcagtagacatctgctggctgtttcatcaggaagagagggataagagagcaagcct 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================================================ gatgagattgggagttattcccagtcttttttgttggaaaatcattggataaagtactcacttcacttgtagctatagagcctgcctatggcatttcctatgtagaaaatatgcaggcagcgttcagcagaccgcctttttatgatacaatggtaagatgaagtcagtagacatctgctggctgtttcatcaggaagagagggataagagagcaagcct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 44 HP_score: -3.3 Tail_Score: -2.92777 Start: 72 End: 92 Full_Region: CTCACTTCACTTGTA GCTATAG AGCCTGC CTATGGC ATTTCCTATGTAGAA .......................................................................GCTATAGAGCCTGCCTATGGC............................................................................................................................... Find igs database================================================ Query_seq: SSA_0599:SSA_0601|SSA_0599:SSA_0601:hypothetical protein:Phosphorylase, Pnp/Udp family, putative:->->:589068..589286 219 gatgagattgggagttattcccagtcttttttgttggaaaatcattggataaagtactcacttcacttgtagctatagagcctgcctatggcatttcctatgtagaaaatatgcaggcagcgttcagcagaccgcctttttatgatacaatggtaagatgaagtcagtagacatctgctggctgtttcatcaggaagagagggataagagagcaagcct Intra-Species Hit: Count: 1 Min: 1 Max: 219 Len: 219 Subject: NC_009009_SSA_0599_SSA_0601|hypothetical protein:Phosphorylase, Pnp/Udp family, putative|POSITIVE:POSITIVE|[589068,589286]|219 HSP 1 e-value: 1.0E-121 bit: 434.0 Len: 219 Query Start:1 Query End:219 Subject Strand: POSITIVE Subject Start: 1 Subject End: 219 gatgagattgggagttattcccagtcttttttgttggaaaatcattggataaagtactcacttcacttgtagctatagagcctgcctatggcatttcctatgtagaaaatatgcaggcagcgttcagcagaccgcctttttatgatacaatggtaagatgaagtcagtagacatctgctggctgtttcatcaggaagagagggataagagagcaagcct gatgagattgggagttattcccagtcttttttgttggaaaatcattggataaagtactcacttcacttgtagctatagagcctgcctatggcatttcctatgtagaaaatatgcaggcagcgttcagcagaccgcctttttatgatacaatggtaagatgaagtcagtagacatctgctggctgtttcatcaggaagagagggataagagagcaagcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAGAUUGGGAGUUAUUCCCAGUCUUUUUUGUUGGAAAAUCAUUGGAUAAAGUACUCACUUCACUUGUAGCUAUAGAGCCUGCCUAUGGCAUUUCCUAUGUAGAAAAUAUGCAGGCAGCGUUCAGCAGACCGCCUUUUUAUGAUACAAUGGUAAGAUGAAGUCAGUAGACAUCUGCUGGCUGUUUCAUCAGGAAGAGAGGGAUAAGAGAGCAAGCCU ...(((((((((((...)))))))))))(((((((.((......)).)))))))..(((.((((..(((((..((((((((((((.(((.((((.....)))).....))).)))))).(((.((....)).)))...)))))).)))))......((((((((((((((....)))))))))...)))))..)))).))).................. (-66.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCUUGCUCUCUUAUCCCUCUCUUCCUGAUGAAACAGCCAGCAGAUGUCUACUGACUUCAUCUUACCAUUGUAUCAUAAAAAGGCGGUCUGCUGAACGCUGCCUGCAUAUUUUCUACAUAGGAAAUGCCAUAGGCAGGCUCUAUAGCUACAAGUGAAGUGAGUACUUUAUCCAAUGAUUUUCCAACAAAAAAGACUGGGAAUAACUCCCAAUCUCAUC ..(((.(((.(.(((((...........))))).).))).))).((((..((((.(((((((.......(((((.(.......((((.((....)).))))((((((.((((((((....))))))))......))))))......).)))))))))))).))))...))))....................(((.(((((.....))))).))).... (-53.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 178 132 229 177 NC_009009:SSA_1920|5end_Phosphotransferase_system,_mannose-specific_EIID,_putative_1909863..1910093_POSITIVE 341 118 77 127 80 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 332 102 66 83 40 NC_009009:SSA_2081|5end_hypothetical_protein_2085309..2085539_POSITIVE 324 147 114 77 37 NC_009009:SSA_0759|5end_Acetylglutamate_kinase,_putative_741841..742071_POSITIVE 323 136 91 58 10 NC_009009:SSA_0040|5end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_46308..46538_POSITIVE 318 140 91 189 137 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 317 119 71 162 120 NC_009009:SSA_2080|5end_hypothetical_protein_2085341..2085571_NEGATIVE 310 135 112 69 40 NC_009009:SSA_2067|5end_hypothetical_protein_2070254..2070484_POSITIVE 310 204 174 48 18 NC_009009:SSA_0898|5end_hypothetical_protein_889863..890093_NEGATIVE 308 120 71 45 5 NC_009009:SSA_1413|5end_GufA-like_protein,_putative_1424919..1425149_NEGATIVE 307 124 82 92 45 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 306 130 81 130 85 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 304 125 83 195 147 NC_009009:SSA_2221|5end_Cps9E,_putative_2223257..2223487_NEGATIVE 303 95 53 153 111 NC_009009:SSA_2131|5end_DNA-binding_protein,_putative_2133949..2134179_POSITIVE 303 194 151 185 142 NC_009009:SSA_1693|5end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1686811..1687041_NEGATIVE 302 197 157 53 13 NC_009009:SSA_2045|5end_Reductase,_putative_2048948..2049178_NEGATIVE 301 140 115 26 3 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 299 198 156 62 13 NC_009009:SSA_1873|5end_S-adenosyl-methyltransferase_mraW,_putative_1870144..1870374_NEGATIVE 296 200 152 77 35 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 295 200 156 190 142 NC_009009:SSA_0650|5end_GTP-binding_protein_TypA/BipA,_putative_632548..632778_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 341 118 77 90 43 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 324 147 114 65 25 NC_009009:SSA_0758|3end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_741909..742059_POSITIVE 323 136 91 71 23 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 310 204 174 143 113 NC_009009:SSA_0898|3end_hypothetical_protein_889768..889918_NEGATIVE 303 95 53 144 102 NC_009009:SSA_2130|3end_hypothetical_protein_2134020..2134170_POSITIVE 302 197 157 44 4 NC_009009:SSA_2046|3end_Uridine_phosphorylase,_putative_2048957..2049107_NEGATIVE 300 118 71 151 110 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 296 200 152 53 1 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 296 200 152 72 30 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 295 135 91 89 34 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 292 210 162 136 73 NC_009009:SSA_0609|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_598247..598397_NEGATIVE 292 203 162 128 82 NC_009009:SSA_0587|3end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_579761..579911_POSITIVE 289 136 93 100 61 NC_009009:SSA_1366|3end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1382296..1382446_NEGATIVE 284 206 166 61 20 NC_009009:SSA_1280|3end_hypothetical_protein_1301108..1301258_NEGATIVE 283 99 56 63 17 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 283 119 71 66 25 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 282 138 92 134 83 NC_009009:SSA_0815|3end_hypothetical_protein_797411..797561_POSITIVE 279 86 44 71 27 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 278 119 72 142 106 NC_009009:SSA_2222|3end_Tyrosine-protein_kinase_Wze,_putative_2223299..2223449_NEGATIVE 277 160 115 105 64 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE