Origin IGS: actttttcttgggttttaagtcatctgggtttcttttgtggaagcccagtttttttcttgcttttcaggggatttttagactttgtaatcggttttttatgcagttttttgttataataaaagttacggaaaaactagaaatgaaaggaaaaggac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtccttttcctttcatttctagtttttccgtaacttttattataacaaaaaactgcataaaaaaccgattacaaagtctaaaaatcccctgaaaagcaagaaaaaaactgggcttccacaaaagaaacccagatgacttaaaacccaagaaaaagt Mask Tandem Repeat Region ================================================ actttttcttgggttttaagtcatctgggtttcttttgtggaagcccagtttttttcttgcttttcaggggatttttagactttgtaatcggttttttatgcagttttttgttataataaaagttacggaaaaactagaaatgaaaggaaaaggac Find is-nt database================================================ Query_seq: SSA_0673:SSA_0674|SSA_0673:SSA_0674:hypothetical protein:Exodeoxyribonuclease VII large subunit, putative:->->:657055..657210 156 actttttcttgggttttaagtcatctgggtttcttttgtggaagcccagtttttttcttgcttttcaggggatttttagactttgtaatcggttttttatgcagttttttgttataataaaagttacggaaaaactagaaatgaaaggaaaaggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0673:SSA_0674|SSA_0673:SSA_0674:hypothetical protein:Exodeoxyribonuclease VII large subunit, putative:->->:657055..657210 156 actttttcttgggttttaagtcatctgggtttcttttgtggaagcccagtttttttcttgcttttcaggggatttttagactttgtaatcggttttttatgcagttttttgttataataaaagttacggaaaaactagaaatgaaaggaaaaggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0673:SSA_0674|SSA_0673:SSA_0674:hypothetical protein:Exodeoxyribonuclease VII large subunit, putative:->->:657055..657210 156 actttttcttgggttttaagtcatctgggtttcttttgtggaagcccagtttttttcttgcttttcaggggatttttagactttgtaatcggttttttatgcagttttttgttataataaaagttacggaaaaactagaaatgaaaggaaaaggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actttttcttgggttttaagtcatctgggtttcttttgtggaagcccagtttttttcttgcttttcaggggatttttagactttgtaatcggttttttatgcagttttttgttataataaaagttacggaaaaactagaaatgaaaggaaaaggac Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 25 End: 114 ........................ M G F F C G S P V F F L L F R G F L D F V I G F L C S F L L .......................................... Protein_Len: 49 Strand: + Start: 9 End: 155 ........ M G F K S S G F L L W K P S F F L A F Q G I F R L C N R F F M Q F F V I I K V T E K L E M K G K G . actttttcttgggttttaagtcatctgggtttcttttgtggaagcccagtttttttcttgcttttcaggggatttttagactttgtaatcggttttttatgcagttttttgttataataaaagttacggaaaaactagaaatgaaaggaaaaggac 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================================================ actttttcttgggttttaagtcatctgggtttcttttgtggaagcccagtttttttcttgcttttcaggggatttttagactttgtaatcggttttttatgcagttttttgttataataaaagttacggaaaaactagaaatgaaaggaaaaggac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0673:SSA_0674|SSA_0673:SSA_0674:hypothetical protein:Exodeoxyribonuclease VII large subunit, putative:->->:657055..657210 156 actttttcttgggttttaagtcatctgggtttcttttgtggaagcccagtttttttcttgcttttcaggggatttttagactttgtaatcggttttttatgcagttttttgttataataaaagttacggaaaaactagaaatgaaaggaaaaggac Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: NC_009009_SSA_0673_SSA_0674|hypothetical protein:Exodeoxyribonuclease VII large subunit, putative|POSITIVE:POSITIVE|[657055,657210]|156 HSP 1 e-value: 1.0E-19 bit: 97.6 Len: 49 Query Start:1 Query End:49 Subject Strand: POSITIVE Subject Start: 1 Subject End: 49 actttttcttgggttttaagtcatctgggtttcttttgtggaagcccag........................................................................................................... actttttcttgggttttaagtcatctgggtttcttttgtggaagcccag........................................................................................................... HSP 2 e-value: 6.0E-18 bit: 91.7 Len: 46 Query Start:111 Query End:156 Subject Strand: POSITIVE Subject Start: 111 Subject End: 156 ..............................................................................................................gttataataaaagttacggaaaaactagaaatgaaaggaaaaggac ..............................................................................................................gttataataaaagttacggaaaaactagaaatgaaaggaaaaggac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUUUUCUUGGGUUUUAAGUCAUCUGGGUUUCUUUUGUGGAAGCCCAGUUUUUUUCUUGCUUUUCAGGGGAUUUUUAGACUUUGUAAUCGGUUUUUUAUGCAGUUUUUUGUUAUAAUAAAAGUUACGGAAAAACUAGAAAUGAAAGGAAAAGGAC .(((((((((..((((((((((..((((((((((.....))))))))))....(..((((.....))))..)......))))).......((((((((.......(((((((....))))))).....)))))))).)))))..)))))))))... (-40.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCCUUUUCCUUUCAUUUCUAGUUUUUCCGUAACUUUUAUUAUAACAAAAAACUGCAUAAAAAACCGAUUACAAAGUCUAAAAAUCCCCUGAAAAGCAAGAAAAAAACUGGGCUUCCACAAAAGAAACCCAGAUGACUUAAAACCCAAGAAAAAGU ...(((((.(((...(((((.(((((((.(((..((((.........))))..)))..........((((....))))............))))))).)))))....(((((.(((.......))).)))))..............))).))))). (-23.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 99 52 143 94 NC_009009:SSA_2011|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012856..2013086_NEGATIVE 313 70 21 222 173 NC_009009:SSA_1863|5end_NH(3)-dependent_NAD(+)_synthetase,_putative_1859413..1859643_NEGATIVE 305 65 21 154 110 NC_009009:SSA_0317|5end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311259..311489_POSITIVE 295 80 31 155 97 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 295 49 7 76 24 NC_009009:SSA_1463|5end_Shikimate_kinase,_putative_1470240..1470470_NEGATIVE 295 82 43 55 9 NC_009009:SSA_0728|5end_Protease,_putative_713688..713918_POSITIVE 293 67 26 64 21 NC_009009:SSA_1144|5end_Beta-N-acetylhexosaminidase,_putative_1175610..1175840_NEGATIVE 283 60 11 130 80 NC_009009:SSA_0053|5end_Beta-galactosidase,_putative_56748..56978_POSITIVE 280 47 5 191 141 NC_009009:SSA_1251|5end_Hydrolase,_HD_superfamily,_putative_1276790..1277020_NEGATIVE 275 69 25 190 156 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 274 110 70 213 171 NC_009009:SSA_1233|5end_Membrane_protein,_YqiH_family,_putative_1256896..1257126_POSITIVE 274 80 31 67 23 NC_009009:SSA_1150|5end_Tautomerase,_putative_1180076..1180306_NEGATIVE 273 70 22 34 1 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 270 69 31 132 98 NC_009009:SSA_2345|5end_hypothetical_protein_2346919..2347149_POSITIVE 270 70 25 69 35 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 268 54 25 167 133 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 266 50 2 197 149 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 264 67 24 65 15 NC_009009:SSA_2275|5end_hypothetical_protein_2275590..2275820_NEGATIVE 262 75 46 40 7 NC_009009:SSA_0767|5end_Diacylglycerol_kinase_catalytic_domain_protein,_putative_747087..747317_POSITIVE 261 50 8 221 176 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 99 52 101 52 NC_009009:SSA_2012|3end_hypothetical_protein_2012898..2013048_NEGATIVE 295 49 7 83 31 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 294 70 27 37 2 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 285 83 45 110 72 NC_009009:SSA_0214|3end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210690..210840_POSITIVE 283 80 33 138 102 NC_009009:SSA_1686|3end_hypothetical_protein_1680470..1680620_POSITIVE 275 57 19 150 111 NC_009009:SSA_0316|3end_hypothetical_protein_311342..311492_POSITIVE 273 63 25 89 52 NC_009009:SSA_1349|3end_Transcriptional_regulator,_biotin_repressor_family,_putative_1366513..1366663_POSITIVE 270 70 25 82 48 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 268 54 25 125 91 NC_009009:SSA_1956|3end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1952644..1952794_NEGATIVE 264 67 24 68 18 NC_009009:SSA_2276|3end_hypothetical_protein_2275587..2275737_NEGATIVE 264 67 24 151 113 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 263 98 55 135 94 NC_009009:SSA_1399|3end_hypothetical_protein_1411659..1411809_NEGATIVE 257 93 51 108 67 NC_009009:SSA_1875|3end_hypothetical_protein_1871168..1871318_POSITIVE 253 59 12 116 51 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 251 49 20 141 118 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 250 59 14 149 106 NC_009009:SSA_1950|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component,_putative_1944566..1944716_NEGATIVE 250 70 24 57 3 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 249 50 11 149 101 NC_009009:SSA_1354|3end_hypothetical_protein_1368555..1368705_NEGATIVE 247 74 34 53 11 NC_009009:SSA_1128|3end_Voltage_gated_chloride_channel_EriC,_putative_1154886..1155036_POSITIVE 246 110 72 87 47 NC_009009:SSA_1055|3end_Conserved_uncharacterized_protein_1071797..1071947_POSITIVE