Origin IGS: aatcaggcactgaaatgaatcagtgcctgattttatatatctaaaacgaaaggaaatcgcgggtaagataaggcaatcaagtcagctaaactacaaaaaggtcagtcgagcataaagcaggactgacacagtcttgtcaaaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattttgacaagactgtgtcagtcctgctttatgctcgactgacctttttgtagtttagctgacttgattgccttatcttacccgcgatttcctttcgttttagatatataaaatcaggcactgattcatttcagtgcctgatt Mask Tandem Repeat Region ================================================ aatcaggcactgaaatgaatcagtgcctgattttatatatctaaaacgaaaggaaatcgcgggtaagataaggcaatcaagtcagctaaactacaaaaaggtcagtcgagcataaagcaggactgacacagtcttgtcaaaatc Find is-nt database================================================ Query_seq: SSA_0169:SSA_0170|SSA_0169:SSA_0170:hypothetical protein:hypothetical protein:-><-:168076..168219 144 aatcaggcactgaaatgaatcagtgcctgattttatatatctaaaacgaaaggaaatcgcgggtaagataaggcaatcaagtcagctaaactacaaaaaggtcagtcgagcataaagcaggactgacacagtcttgtcaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0169:SSA_0170|SSA_0169:SSA_0170:hypothetical protein:hypothetical protein:-><-:168076..168219 144 aatcaggcactgaaatgaatcagtgcctgattttatatatctaaaacgaaaggaaatcgcgggtaagataaggcaatcaagtcagctaaactacaaaaaggtcagtcgagcataaagcaggactgacacagtcttgtcaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0169:SSA_0170|SSA_0169:SSA_0170:hypothetical protein:hypothetical protein:-><-:168076..168219 144 aatcaggcactgaaatgaatcagtgcctgattttatatatctaaaacgaaaggaaatcgcgggtaagataaggcaatcaagtcagctaaactacaaaaaggtcagtcgagcataaagcaggactgacacagtcttgtcaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatcaggcactgaaatgaatcagtgcctgattttatatatctaaaacgaaaggaaatcgcgggtaagataaggcaatcaagtcagctaaactacaaaaaggtcagtcgagcataaagcaggactgacacagtcttgtcaaaatc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 23 End: 112 ...................... M P D F I Y L K R K E I A G K I R Q S S Q L N Y K K V S R A ................................ aatcaggcactgaaatgaatcagtgcctgattttatatatctaaaacgaaaggaaatcgcgggtaagataaggcaatcaagtcagctaaactacaaaaaggtcagtcgagcataaagcaggactgacacagtcttgtcaaaatc 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================================================ aatcaggcactgaaatgaatcagtgcctgattttatatatctaaaacgaaaggaaatcgcgggtaagataaggcaatcaagtcagctaaactacaaaaaggtcagtcgagcataaagcaggactgacacagtcttgtcaaaatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0169:SSA_0170|SSA_0169:SSA_0170:hypothetical protein:hypothetical protein:-><-:168076..168219 144 aatcaggcactgaaatgaatcagtgcctgattttatatatctaaaacgaaaggaaatcgcgggtaagataaggcaatcaagtcagctaaactacaaaaaggtcagtcgagcataaagcaggactgacacagtcttgtcaaaatc Intra-Species Hit: Count: 1 Min: 1 Max: 144 Len: 144 Subject: NC_009009_SSA_0169_SSA_0170|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[168076,168219]|144 HSP 1 e-value: 2.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 aatcaggcactgaaatgaatcagtgcctgattttatatatctaaaacgaaaggaaatcgcgggtaagataaggcaatcaagtcagctaaactacaaaaaggtcagtcgagcataaagcaggactgacacagtcttgtcaaaatc aatcaggcactgaaatgaatcagtgcctgattttatatatctaaaacgaaaggaaatcgcgggtaagataaggcaatcaagtcagctaaactacaaaaaggtcagtcgagcataaagcaggactgacacagtcttgtcaaaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCAGGCACUGAAAUGAAUCAGUGCCUGAUUUUAUAUAUCUAAAACGAAAGGAAAUCGCGGGUAAGAUAAGGCAAUCAAGUCAGCUAAACUACAAAAAGGUCAGUCGAGCAUAAAGCAGGACUGACACAGUCUUGUCAAAAUC (((((((((((((......))))))))))))).....(((((....(....)........))))).((((((((.....((....)).............(((((((..((.....))..)))))))...))))))))...... (-46.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUUGACAAGACUGUGUCAGUCCUGCUUUAUGCUCGACUGACCUUUUUGUAGUUUAGCUGACUUGAUUGCCUUAUCUUACCCGCGAUUUCCUUUCGUUUUAGAUAUAUAAAAUCAGGCACUGAUUCAUUUCAGUGCCUGAUU .......((((((..(.(((((((..((.....))..)))))))).))))))......................(((((.....((((.......))))...))))).....(((((((((((((......))))))))))))) (-45.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 139 96 53 9 NC_009009:SSA_0318|5end_Secreted_metalloendopeptidase_Gcp_311701..311931_POSITIVE 322 120 71 76 29 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 304 128 81 68 26 NC_009009:SSA_0758|5end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_740636..740866_POSITIVE 285 87 41 66 25 NC_009009:SSA_0564|5end_Potential_aminotransferase,_putative_555694..555924_POSITIVE 284 112 71 57 13 NC_009009:SSA_0731|5end_Integral_membrane_protein,_putative_715065..715295_POSITIVE 277 87 50 229 193 NC_009009:SSA_1432|5end_HflX_GTPase,_putative_1439901..1440131_NEGATIVE 271 137 99 172 127 NC_009009:SSA_0841|5end_hypothetical_protein_826935..827165_POSITIVE 266 119 71 168 105 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 266 133 97 196 161 NC_009009:SSA_1643|5end_hypothetical_protein_1645269..1645499_NEGATIVE 266 136 99 78 34 NC_009009:SSA_1117|5end_hypothetical_protein_1142743..1142973_POSITIVE 263 135 98 161 108 NC_009009:SSA_0273|5end_hypothetical_protein_267071..267301_POSITIVE 260 94 52 64 14 NC_009009:SSA_0290|5end_hypothetical_protein_285229..285459_NEGATIVE 260 120 72 112 68 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 258 137 94 170 127 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 257 49 5 66 22 NC_009009:SSA_2360|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase,_putative_2363779..2364009_NEGATIVE 257 133 94 135 103 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 257 138 96 168 128 NC_009009:SSA_0449|5end_Aminopeptidase_P;_XAA-pro_aminopeptidase,_putative_449464..449694_POSITIVE 254 118 71 62 21 NC_009009:SSA_0584|5end_hypothetical_protein_575806..576036_POSITIVE 253 140 93 164 127 NC_009009:SSA_0907|5end_Fibronectin-binding_protein_A,_putative_919217..919447_NEGATIVE 250 139 99 215 179 NC_009009:SSA_1865|5end_Thioredoxin_reductase,_putative_1861892..1862122_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 439 37 1 95 59 NC_009009:SSA_0169|3end_hypothetical_protein_168015..168165_POSITIVE 329 139 96 63 19 NC_009009:SSA_0317|3end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311791..311941_POSITIVE 327 87 51 90 53 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 322 120 71 48 1 NC_009009:SSA_0220|3end_PTS_system,_mannose-specific_IIB_component,_putative_216422..216572_POSITIVE 306 105 61 74 22 NC_009009:SSA_0730|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_715167..715317_POSITIVE 304 128 81 50 8 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 290 112 71 119 78 NC_009009:SSA_2354|3end_hypothetical_protein_2355605..2355755_NEGATIVE 281 110 66 150 106 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 260 120 72 86 42 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 257 133 94 60 28 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 251 118 76 145 98 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 250 139 99 149 113 NC_009009:SSA_1866|3end_hypothetical_protein_1861958..1862108_NEGATIVE 249 124 82 74 21 NC_009009:SSA_0314|3end_Nucleoside-diphosphate-sugar_epimerase,_putative_308967..309117_NEGATIVE 247 137 112 68 42 NC_009009:SSA_0066|3end_hypothetical_protein_68095..68245_POSITIVE 246 139 101 93 52 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 245 135 104 74 37 NC_009009:SSA_1156|3end_hypothetical_protein_1185616..1185766_POSITIVE 244 139 99 149 114 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 242 95 56 41 4 NC_009009:SSA_0238|3end_hypothetical_protein_233031..233181_POSITIVE 240 140 100 55 12 NC_009009:SSA_0434|3end_Glutamate_formiminotransferase,_putative_435669..435819_NEGATIVE 239 64 24 56 16 NC_009009:SSA_2367|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368845..2368995_NEGATIVE