Origin IGS: gggaacttttgaattgcttttctaatgagaagcctgttcagataacctttcttgaaccgaaaataaacaaaataaaaggggacagagtagactcacccccttctattttgtttttaaacgagtttattaatcggtttaatagattgctttaaaaacaaaaaaggagaccaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattggtctccttttttgtttttaaagcaatctattaaaccgattaataaactcgtttaaaaacaaaatagaagggggtgagtctactctgtccccttttattttgtttattttcggttcaagaaaggttatctgaacaggcttctcattagaaaagcaattcaaaagttccc Mask Tandem Repeat Region ================================================ gggaacttttgaattgcttttctaatgagaagcctgttcagataacctttcttgaaccgaaaataaacaaaataaaaggggacagagtagactcacccccttctattttgtttttaaacgagtttattaatcggtttaatagattgctttaaaaacaaaaaaggagaccaatc Find is-nt database================================================ Query_seq: SSA_0127:SSA_0128|SSA_0127:SSA_0128:Multispanning membrane protein, translocator of proteins, putative:Adenylate kinase, putative:->->:119168..119340 173 gggaacttttgaattgcttttctaatgagaagcctgttcagataacctttcttgaaccgaaaataaacaaaataaaaggggacagagtagactcacccccttctattttgtttttaaacgagtttattaatcggtttaatagattgctttaaaaacaaaaaaggagaccaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0127:SSA_0128|SSA_0127:SSA_0128:Multispanning membrane protein, translocator of proteins, putative:Adenylate kinase, putative:->->:119168..119340 173 gggaacttttgaattgcttttctaatgagaagcctgttcagataacctttcttgaaccgaaaataaacaaaataaaaggggacagagtagactcacccccttctattttgtttttaaacgagtttattaatcggtttaatagattgctttaaaaacaaaaaaggagaccaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0127:SSA_0128|SSA_0127:SSA_0128:Multispanning membrane protein, translocator of proteins, putative:Adenylate kinase, putative:->->:119168..119340 173 gggaacttttgaattgcttttctaatgagaagcctgttcagataacctttcttgaaccgaaaataaacaaaataaaaggggacagagtagactcacccccttctattttgtttttaaacgagtttattaatcggtttaatagattgctttaaaaacaaaaaaggagaccaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggaacttttgaattgcttttctaatgagaagcctgttcagataacctttcttgaaccgaaaataaacaaaataaaaggggacagagtagactcacccccttctattttgtttttaaacgagtttattaatcggtttaatagattgctttaaaaacaaaaaaggagaccaatc Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 9 End: 149 ........ M N C F S N E K P V Q I T F L E P K I N K I K G D R V D S P P S I L F L N E F I N R F N R L L ........................ gggaacttttgaattgcttttctaatgagaagcctgttcagataacctttcttgaaccgaaaataaacaaaataaaaggggacagagtagactcacccccttctattttgtttttaaacgagtttattaatcggtttaatagattgctttaaaaacaaaaaaggagaccaatc 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================================================ gggaacttttgaattgcttttctaatgagaagcctgttcagataacctttcttgaaccgaaaataaacaaaataaaaggggacagagtagactcacccccttctattttgtttttaaacgagtttattaatcggtttaatagattgctttaaaaacaaaaaaggagaccaatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -5.7 Tail_Score: -4.58685 Start: 68 End: 110 Full_Region: TGAACCGAAAATAAA CAAAATAAAAGGGGACAGAG TAGA CTCACCCCCTTCTATTTTG TTTTTAAACGAGTTT ...................................................................CAAAATAAAAGGGGACAGAGTAGACTCACCCCCTTCTATTTTG............................................................... TransTerm Strand: - Conf: 100 HP_score: -12.3 Tail_Score: -4.72188 Start: 68 End: 110 Full_Region: aaactcgtttaaaaa caaaatagaagggggtgag tcta ctctgtccccttttattttg tttattttcggttca ...................................................................caaaatagaagggggtgagtctactctgtccccttttattttg............................................................... TransTerm Strand: - Conf: 85 HP_score: -6.4 Tail_Score: -5.26247 Start: 73 End: 105 Full_Region: cgtttaaaaacaaaa tagaagggggtgag tcta ctctgtcccctttta ttttgtttattttcg ........................................................................tagaagggggtgagtctactctgtcccctttta.................................................................... TransTerm Strand: - Conf: 79 HP_score: -4.1 Tail_Score: -5.3689 Start: 78 End: 100 Full_Region: aaaaacaaaatagaa gggggtgag tcta ctctgtcccc ttttattttgtttat .............................................................................gggggtgagtctactctgtcccc......................................................................... TransTerm Strand: + Conf: 45 HP_score: -2.0 Tail_Score: -3.51232 Start: 123 End: 143 Full_Region: TTGTTTTTAAACGAG TTTATTAA TCGGT TTAATAGA TTGCTTTAAAAACAA ..........................................................................................................................TTTATTAATCGGTTTAATAGA.............................. Find igs database================================================ Query_seq: SSA_0127:SSA_0128|SSA_0127:SSA_0128:Multispanning membrane protein, translocator of proteins, putative:Adenylate kinase, putative:->->:119168..119340 173 gggaacttttgaattgcttttctaatgagaagcctgttcagataacctttcttgaaccgaaaataaacaaaataaaaggggacagagtagactcacccccttctattttgtttttaaacgagtttattaatcggtttaatagattgctttaaaaacaaaaaaggagaccaatc Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: NC_009009_SSA_0127_SSA_0128|Multispanning membrane protein, translocator of proteins, putative:Adenylate kinase, putative|POSITIVE:POSITIVE|[119168,119340]|173 HSP 1 e-value: 6.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 gggaacttttgaattgcttttctaatgagaagcctgttcagataacctttcttgaaccgaaaataaacaaaataaaaggggacagagtagactcacccccttctattttgtttttaaacgagtttattaatcggtttaatagattgcttt....................... gggaacttttgaattgcttttctaatgagaagcctgttcagataacctttcttgaaccgaaaataaacaaaataaaaggggacagagtagactcacccccttctattttgtttttaaacgagtttattaatcggtttaatagattgcttt....................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAACUUUUGAAUUGCUUUUCUAAUGAGAAGCCUGUUCAGAUAACCUUUCUUGAACCGAAAAUAAACAAAAUAAAAGGGGACAGAGUAGACUCACCCCCUUCUAUUUUGUUUUUAAACGAGUUUAUUAAUCGGUUUAAUAGAUUGCUUU ((.....(((((((.(((((((....)))))))..)))))))...))....(((((((((....((((((((((.((((((...(((....)))..)))))).)))))))))).((((....))))....)))))))))........... (-46.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGCAAUCUAUUAAACCGAUUAAUAAACUCGUUUAAAAACAAAAUAGAAGGGGGUGAGUCUACUCUGUCCCCUUUUAUUUUGUUUAUUUUCGGUUCAAGAAAGGUUAUCUGAACAGGCUUCUCAUUAGAAAAGCAAUUCAAAAGUUCCC .....(((((.((.((((((....((((....)))).(((((((((((((((((..(((....)))...)))))))))))))))))....)))))).))...)))))...((((...((((.((....)).))))..))))......... (-41.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 116 77 120 73 NC_009009:SSA_0137|5end_ABC_transporter_(permease),_Zn_porter,_putative_131717..131947_POSITIVE 284 117 75 228 186 NC_009009:SSA_1340|5end_Zn/Mn_ABC-type_porter_lipoprotein,_putative_1356372..1356602_NEGATIVE 256 112 74 171 131 NC_009009:SSA_0903|5end_NAD(P)H_dehydrogenase_(quinone),_putative_893242..893472_POSITIVE 254 60 15 198 158 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 252 60 26 61 24 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 250 49 6 131 82 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 247 109 71 40 1 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 246 59 15 229 194 NC_009009:SSA_0226|5end_60_kDa_chaperonin_218947..219177_POSITIVE 243 130 83 185 142 NC_009009:SSA_1415|5end_Oxidoreductase,_putative_1426508..1426738_NEGATIVE 240 98 53 53 3 NC_009009:SSA_1121|5end_Cytochrome_C-type_biogenesis_protein,_putative_1147149..1147379_POSITIVE 240 60 26 102 60 NC_009009:SSA_0995|5end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_995716..995946_POSITIVE 235 55 13 185 143 NC_009009:SSA_0832|5end_SecY-like_protein,_putative_816708..816938_POSITIVE 232 47 1 229 187 NC_009009:SSA_1900|5end_N_utilization_substance_protein_A,_putative_1896012..1896242_NEGATIVE 232 106 75 85 50 NC_009009:SSA_1751|5end_Dextran_glucosidase,_alpha_amylase_family,_putative_1739801..1740031_NEGATIVE 232 99 76 211 185 NC_009009:SSA_1264|5end_hypothetical_protein_1290042..1290272_NEGATIVE 231 42 15 126 96 NC_009009:SSA_0597|5end_hypothetical_protein_587566..587796_POSITIVE 231 61 25 75 44 NC_009009:SSA_0419|5end_Alpha-galactosidase,_putative_416213..416443_POSITIVE 228 120 79 201 141 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 227 125 81 80 36 NC_009009:SSA_1825|5end_hypothetical_protein_1812951..1813181_POSITIVE 226 138 93 172 121 NC_009009:SSA_0996|5end_cGMP-specific_phosphodiesterase,_putative_996282..996512_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 116 77 127 80 NC_009009:SSA_0136|3end_ABC_transporter,_Zn_porter,_putative_131804..131954_POSITIVE 256 112 74 95 55 NC_009009:SSA_0901|3end_Alpha-acetolactate_decarboxylase,_putative_893246..893396_POSITIVE 252 60 26 83 46 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 250 49 6 84 35 NC_009009:SSA_0457|3end_Fructokinase,_putative_461642..461792_POSITIVE 232 106 75 74 39 NC_009009:SSA_1752|3end_Phosphotransferase_system,_trehalose-specific_IIBC_component,_putative_1739812..1739962_NEGATIVE 232 99 76 69 43 NC_009009:SSA_1265|3end_50S_ribosomal_protein_L19,_putative_1290184..1290334_NEGATIVE 227 53 24 89 57 NC_009009:SSA_0908|3end_ABC-type_uncharacterized_transport_system,_periplasmic_component,_putative_920787..920937_POSITIVE 226 138 93 142 91 NC_009009:SSA_0995|3end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_996332..996482_POSITIVE 225 113 75 73 35 NC_009009:SSA_0779|3end_Glycogen_phosphorylase,_putative_764685..764835_POSITIVE 222 55 14 137 95 NC_009009:SSA_0583|3end_Nucleotidyltransferase,_putative_575679..575829_POSITIVE 222 113 77 101 60 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 221 57 16 58 15 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 221 112 71 76 30 NC_009009:SSA_0233|3end_Permease,_putative_228179..228329_POSITIVE 220 60 26 38 8 NC_009009:SSA_1715|3end_Phosphoserine_aminotransferase,_putative_1701397..1701547_NEGATIVE 220 122 91 147 108 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 220 103 76 126 93 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 219 59 14 78 27 NC_009009:SSA_1083|3end_Conserved_uncharacterized_protein_1101752..1101902_POSITIVE 219 54 13 151 110 NC_009009:SSA_0831|3end_Nucleotide_sugar_synthetase-like_protein,_putative_816755..816905_POSITIVE 216 111 72 87 43 NC_009009:SSA_2271|3end_hypothetical_protein_2272238..2272388_NEGATIVE 215 59 15 63 1 NC_009009:SSA_1432|3end_HflX_GTPase,_putative_1438663..1438813_NEGATIVE