Origin IGS: tgctcaatgaaaatcatcagcaaacatagaaagctaatgcagtcagtgctcaagtagagcaatctggtttgaggagattttttgagaatagagaaaggatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatcctttctctattctcaaaaaatctcctcaaaccagattgctctacttgagcactgactgcattagctttctatgtttgctgatgattttcattgagca Mask Tandem Repeat Region ================================================ tgctcaatgaaaatcatcagcaaacatagaaagctaatgcagtcagtgctcaagtagagcaatctggtttgaggagattttttgagaatagagaaaggatttt Find is-nt database================================================ Query_seq: SSA_0689:SSA_0690|SSA_0689:SSA_0690:Penicillin-binding protein 2B, putative:Recombinational DNA repair protein (RecF pathway), putative:->->:674469..674571 103 tgctcaatgaaaatcatcagcaaacatagaaagctaatgcagtcagtgctcaagtagagcaatctggtttgaggagattttttgagaatagagaaaggatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0689:SSA_0690|SSA_0689:SSA_0690:Penicillin-binding protein 2B, putative:Recombinational DNA repair protein (RecF pathway), putative:->->:674469..674571 103 tgctcaatgaaaatcatcagcaaacatagaaagctaatgcagtcagtgctcaagtagagcaatctggtttgaggagattttttgagaatagagaaaggatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0689:SSA_0690|SSA_0689:SSA_0690:Penicillin-binding protein 2B, putative:Recombinational DNA repair protein (RecF pathway), putative:->->:674469..674571 103 tgctcaatgaaaatcatcagcaaacatagaaagctaatgcagtcagtgctcaagtagagcaatctggtttgaggagattttttgagaatagagaaaggatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgctcaatgaaaatcatcagcaaacatagaaagctaatgcagtcagtgctcaagtagagcaatctggtttgaggagattttttgagaatagagaaaggatttt Predict ORF larger than 30AA ================================================ tgctcaatgaaaatcatcagcaaacatagaaagctaatgcagtcagtgctcaagtagagcaatctggtttgaggagattttttgagaatagagaaaggatttt 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================================================ tgctcaatgaaaatcatcagcaaacatagaaagctaatgcagtcagtgctcaagtagagcaatctggtttgaggagattttttgagaatagagaaaggatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0689:SSA_0690|SSA_0689:SSA_0690:Penicillin-binding protein 2B, putative:Recombinational DNA repair protein (RecF pathway), putative:->->:674469..674571 103 tgctcaatgaaaatcatcagcaaacatagaaagctaatgcagtcagtgctcaagtagagcaatctggtttgaggagattttttgagaatagagaaaggatttt Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_009009_SSA_0689_SSA_0690|Penicillin-binding protein 2B, putative:Recombinational DNA repair protein (RecF pathway), putative|POSITIVE:POSITIVE|[674469,674571]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 tgctcaatgaaaatcatcagcaaacatagaaagctaatgcagtcagtgctcaagtagagcaatctggtttgaggagattttttgagaatagagaaaggatttt tgctcaatgaaaatcatcagcaaacatagaaagctaatgcagtcagtgctcaagtagagcaatctggtttgaggagattttttgagaatagagaaaggatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUCAAUGAAAAUCAUCAGCAAACAUAGAAAGCUAAUGCAGUCAGUGCUCAAGUAGAGCAAUCUGGUUUGAGGAGAUUUUUUGAGAAUAGAGAAAGGAUUUU ..((((..(((((((.((..(((((.((((..((....))......(((((.....))))).)))))))))..)))))))))))))................. (-26.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCCUUUCUCUAUUCUCAAAAAAUCUCCUCAAACCAGAUUGCUCUACUUGAGCACUGACUGCAUUAGCUUUCUAUGUUUGCUGAUGAUUUUCAUUGAGCA .................(((((((((((((..(((((.....(((((.....)))))..((..((....))..))...)))))..)).))))))..))))).. (-20.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 76 33 219 182 NC_009009:SSA_1890|5end_Acetyltransferase,_putative_1888145..1888375_NEGATIVE 320 74 32 158 122 NC_009009:SSA_1907|5end_hypothetical_protein_1900446..1900676_POSITIVE 315 60 13 55 8 NC_009009:SSA_0167|5end_Hypothetical_protein_(Asparagine/proline-rich)_165254..165484_POSITIVE 305 70 24 200 148 NC_009009:SSA_1565|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1569309..1569539_NEGATIVE 288 80 33 85 36 NC_009009:SSA_0243|5end_Cyclo-nucleotide_phosphodiesterase,_putative_238235..238465_NEGATIVE 281 59 13 192 159 NC_009009:SSA_1691|5end_Transcriptional_regulator,_XRE_family,_putative_1683281..1683511_POSITIVE 280 60 13 64 8 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 279 99 51 69 24 NC_009009:SSA_1672|5end_hypothetical_protein_1670389..1670619_NEGATIVE 276 76 33 177 140 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 273 88 41 168 115 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 272 60 14 154 107 NC_009009:SSA_1744|5end_Iron_compound_ABC_transporter,_permease_protein,_putative_1730915..1731145_POSITIVE 270 60 19 195 139 NC_009009:SSA_1323|5end_hypothetical_protein_1340450..1340680_NEGATIVE 270 76 32 43 8 NC_009009:SSA_0400|5end_hypothetical_protein_398251..398481_NEGATIVE 266 31 4 231 204 NC_009009:SSA_0345|5end_hypothetical_protein_338803..339033_POSITIVE 263 75 33 219 174 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 262 85 42 217 174 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 260 76 32 43 3 NC_009009:SSA_1368|5end_hypothetical_protein_1384077..1384307_NEGATIVE 257 88 41 228 176 NC_009009:SSA_2074|5end_Preprotein_translocase_subunit_YajC,_putative_2076935..2077165_NEGATIVE 257 67 26 168 123 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 256 79 32 44 3 NC_009009:SSA_1369|5end_FmtA-like_protein,_putative_1385929..1386159_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 74 32 148 112 NC_009009:SSA_1906|3end_Diadenosine_tetraphosphate_(Ap4A)_hydrolase_(histidine_triad_protein,_cell-cycle_regulation),_putative_1900516..1900666_POSITIVE 273 76 31 78 43 NC_009009:SSA_0036|3end_Secreted_protein,_possible_function_in_cell-wall_metabolism_(amidase),_putative_42050..42200_NEGATIVE 263 60 20 48 2 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 262 79 33 84 36 NC_009009:SSA_0705|3end_hypothetical_protein_690552..690702_NEGATIVE 259 60 13 130 72 NC_009009:SSA_1280|3end_hypothetical_protein_1301108..1301258_NEGATIVE 256 70 33 148 109 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 256 46 1 53 9 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 255 75 41 150 106 NC_009009:SSA_1094|3end_GTP-binding_protein,_putative_1112243..1112393_POSITIVE 250 49 3 59 8 NC_009009:SSA_0741|3end_Acetylornithine_deacetylase/Succinyl-diaminopimelate_desuccinylase,_putative_725190..725340_POSITIVE 247 79 35 117 76 NC_009009:SSA_2205|3end_Transcription_antitermination_factor_NusG,_putative_2205564..2205714_NEGATIVE 246 81 48 89 49 NC_009009:SSA_1793|3end_Histidine_kinase_(sensor_protein),_putative_1775126..1775276_NEGATIVE 246 88 48 47 9 NC_009009:SSA_0369|3end_NADP-specific_glutamate_dehydrogenase,_putative_359723..359873_NEGATIVE 246 60 14 133 80 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 245 74 40 70 36 NC_009009:SSA_1800|3end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1781037..1781187_NEGATIVE 245 68 21 121 79 NC_009009:SSA_0302|3end_Phosphoglycerate_kinase,_putative_296166..296316_POSITIVE 244 50 6 70 35 NC_009009:SSA_1854|3end_Conserved_uncharacterized_protein_1849433..1849583_NEGATIVE 241 79 31 58 9 NC_009009:SSA_0220|3end_PTS_system,_mannose-specific_IIB_component,_putative_216422..216572_POSITIVE 239 79 31 123 71 NC_009009:SSA_0845|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_829339..829489_NEGATIVE 239 73 31 150 107 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 238 68 23 131 79 NC_009009:SSA_1993|3end_Conserved_uncharacterized_protein_1990380..1990530_NEGATIVE