Origin IGS: aagccttcaacagtatgagagagctctggttcttgatagcgattcagcttgtttgggaccggagctgctctgtactgggggcgtggtaaaaacaaagctagaaaggagtacctccac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtggaggtactcctttctagctttgtttttaccacgcccccagtacagagcagctccggtcccaaacaagctgaatcgctatcaagaaccagagctctctcatactgttgaaggctt Mask Tandem Repeat Region ================================================ aagccttcaacagtatgagagagctctggttcttgatagcgattcagcttgtttgggaccggagctgctctgtactgggggcgtggtaaaaacaaagctagaaaggagtacctccac Find is-nt database================================================ Query_seq: SSA_0478:SSA_0479|SSA_0478:SSA_0479:Cobalt transport protein cbiN, putative:CbiQ protein, putative:->->:480448..480564 117 aagccttcaacagtatgagagagctctggttcttgatagcgattcagcttgtttgggaccggagctgctctgtactgggggcgtggtaaaaacaaagctagaaaggagtacctccac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0478:SSA_0479|SSA_0478:SSA_0479:Cobalt transport protein cbiN, putative:CbiQ protein, putative:->->:480448..480564 117 aagccttcaacagtatgagagagctctggttcttgatagcgattcagcttgtttgggaccggagctgctctgtactgggggcgtggtaaaaacaaagctagaaaggagtacctccac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0478:SSA_0479|SSA_0478:SSA_0479:Cobalt transport protein cbiN, putative:CbiQ protein, putative:->->:480448..480564 117 aagccttcaacagtatgagagagctctggttcttgatagcgattcagcttgtttgggaccggagctgctctgtactgggggcgtggtaaaaacaaagctagaaaggagtacctccac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagccttcaacagtatgagagagctctggttcttgatagcgattcagcttgtttgggaccggagctgctctgtactgggggcgtggtaaaaacaaagctagaaaggagtacctccac Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 26 End: 115 ......................... M V L D S D S A C L G P E L L C T G G V V K T K L E R S T S .. Protein_Len: 36 Strand: - Start: 10 End: 117 ......... C Y S L A R T R S L S E A Q K P G S S S Q V P P T T F V F S S L L V E M Protein_Len: 31 Strand: - Start: 3 End: 95 .. G E V T H S L E P E Q Y R N L K N P V P A A R Y Q P R P L F M ...................... aagccttcaacagtatgagagagctctggttcttgatagcgattcagcttgtttgggaccggagctgctctgtactgggggcgtggtaaaaacaaagctagaaaggagtacctccac 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================================================ aagccttcaacagtatgagagagctctggttcttgatagcgattcagcttgtttgggaccggagctgctctgtactgggggcgtggtaaaaacaaagctagaaaggagtacctccac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 39 HP_score: -2.4 Tail_Score: -2.78596 Start: 19 End: 70 Full_Region: CCTTCAACAGTATGA GAGAGCTCTGGTTCTTGATAGC GATTCA GCTTGTTTGGGACCGGAGCTGCTC TGTACTGGGGGCGTG ..................GAGAGCTCTGGTTCTTGATAGCGATTCAGCTTGTTTGGGACCGGAGCTGCTC............................................... Find igs database================================================ Query_seq: SSA_0478:SSA_0479|SSA_0478:SSA_0479:Cobalt transport protein cbiN, putative:CbiQ protein, putative:->->:480448..480564 117 aagccttcaacagtatgagagagctctggttcttgatagcgattcagcttgtttgggaccggagctgctctgtactgggggcgtggtaaaaacaaagctagaaaggagtacctccac Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_009009_SSA_0478_SSA_0479|Cobalt transport protein cbiN, putative:CbiQ protein, putative|POSITIVE:POSITIVE|[480448,480564]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 aagccttcaacagtatgagagagctctggttcttgatagcgattcagcttgtttgggaccggagctgctctgtactgggggcgtggtaaaaacaaagctagaaaggagtacctccac aagccttcaacagtatgagagagctctggttcttgatagcgattcagcttgtttgggaccggagctgctctgtactgggggcgtggtaaaaacaaagctagaaaggagtacctccac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCCUUCAACAGUAUGAGAGAGCUCUGGUUCUUGAUAGCGAUUCAGCUUGUUUGGGACCGGAGCUGCUCUGUACUGGGGGCGUGGUAAAAACAAAGCUAGAAAGGAGUACCUCCAC ..((((....((((((.((((((((((((((((.((((((......)).)))).)))))))))))).)))))))))).))))......................((((...)))).. (-47.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGGAGGUACUCCUUUCUAGCUUUGUUUUUACCACGCCCCCAGUACAGAGCAGCUCCGGUCCCAAACAAGCUGAAUCGCUAUCAAGAACCAGAGCUCUCUCAUACUGUUGAAGGCUU ..((((...))))......................(((..(((((.((((.(((((.(((........(((......))).......))).)))))))))..))))).....))).. (-28.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 67 22 203 137 NC_009009:SSA_0606|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_594532..594762_NEGATIVE 364 99 53 77 20 NC_009009:SSA_1536|5end_Biotin_synthase,_putative_1543609..1543839_POSITIVE 363 84 43 41 1 NC_009009:SSA_0691|5end_D-ala,D-ala_ligase,_putative_675233..675463_POSITIVE 353 68 27 136 94 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 347 79 31 65 6 NC_009009:SSA_0291|5end_Oxidoreductase,_putative_285362..285592_POSITIVE 343 84 46 82 35 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 339 98 51 221 173 NC_009009:SSA_0250|5end_GTP_pyrophosphokinase,_putative_242167..242397_POSITIVE 338 83 46 87 53 NC_009009:SSA_2081|5end_hypothetical_protein_2085309..2085539_POSITIVE 336 69 22 198 151 NC_009009:SSA_1794|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1777049..1777279_NEGATIVE 336 86 41 67 26 NC_009009:SSA_0387|5end_Transcriptional_regulator,_GntR_family,_putative_382343..382573_NEGATIVE 334 80 32 167 115 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 334 87 41 149 83 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 331 86 41 125 74 NC_009009:SSA_2157|5end_ATP-dependent_serine_protease,_putative_2158241..2158471_NEGATIVE 330 99 58 57 9 NC_009009:SSA_0203|5end_hypothetical_protein_201322..201552_POSITIVE 329 102 61 59 28 NC_009009:SSA_2059|5end_16S_rRNA_uridine-516_pseudouridylate_synthase,_putative_2061222..2061452_NEGATIVE 329 89 43 171 118 NC_009009:SSA_1907|5end_hypothetical_protein_1900446..1900676_POSITIVE 325 70 21 76 17 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 325 84 51 48 1 NC_009009:SSA_0761|5end_Transcriptional_regulator,_XRE_family,_putative_743877..744107_POSITIVE 324 68 22 215 171 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 323 83 43 191 140 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 68 29 148 109 NC_009009:SSA_0209|3end_Glutamyl_aminopeptidase,_putative_206572..206722_NEGATIVE 386 70 22 72 25 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 371 67 22 145 79 NC_009009:SSA_0607|3end_ABC_transporter,_permease_component,_putative_594590..594740_NEGATIVE 343 84 46 89 42 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 340 86 46 148 98 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 339 98 51 89 41 NC_009009:SSA_0249|3end_hypothetical_protein_242115..242265_POSITIVE 337 50 5 149 102 NC_009009:SSA_0973|3end_hypothetical_protein_980687..980837_POSITIVE 334 87 41 144 78 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 330 99 58 57 9 NC_009009:SSA_0202|3end_hypothetical_protein_201402..201552_POSITIVE 329 102 61 47 16 NC_009009:SSA_2060|3end_Arabinose_efflux_permease,_putative_2061234..2061384_NEGATIVE 323 86 43 151 106 NC_009009:SSA_1440|3end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444407..1444557_NEGATIVE 319 86 41 57 2 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 319 79 33 149 100 NC_009009:SSA_0936|3end_FAD_synthase,_putative_946151..946301_POSITIVE 318 90 46 144 102 NC_009009:SSA_2018|3end_hypothetical_protein_2017464..2017614_NEGATIVE 313 78 32 141 96 NC_009009:SSA_1906|3end_Diadenosine_tetraphosphate_(Ap4A)_hydrolase_(histidine_triad_protein,_cell-cycle_regulation),_putative_1900516..1900666_POSITIVE 311 86 48 64 8 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 310 84 46 150 100 NC_009009:SSA_1052|3end_hypothetical_protein_1066846..1066996_NEGATIVE 309 110 61 62 18 NC_009009:SSA_1555|3end_Glucose-6-phosphate_1-dehydrogenase,_putative_1558482..1558632_POSITIVE 309 86 43 142 104 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 308 100 59 97 61 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE