Origin IGS: aatcttaggcaaaatcaagacaaccagagaagaaactattactgtcagcaaattggacaagacaacataggaaaaattagctattatttttttaaatccaccagacaaatttgccctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagggcaaatttgtctggtggatttaaaaaaataatagctaatttttcctatgttgtcttgtccaatttgctgacagtaatagtttcttctctggttgtcttgattttgcctaagatt Mask Tandem Repeat Region ================================================ aatcttaggcaaaatcaagacaaccagagaagaaactattactgtcagcaaattggacaagacaacataggaaaaattagctattatttttttaaatccaccagacaaatttgccctc Find is-nt database================================================ Query_seq: SSA_2212:SSA_2213|SSA_2212:SSA_2213:Possible polysaccharide transport protein, putative:Nucleotide sugar dehydratase, putative:<-<-:2214019..2214136 118 aatcttaggcaaaatcaagacaaccagagaagaaactattactgtcagcaaattggacaagacaacataggaaaaattagctattatttttttaaatccaccagacaaatttgccctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2212:SSA_2213|SSA_2212:SSA_2213:Possible polysaccharide transport protein, putative:Nucleotide sugar dehydratase, putative:<-<-:2214019..2214136 118 aatcttaggcaaaatcaagacaaccagagaagaaactattactgtcagcaaattggacaagacaacataggaaaaattagctattatttttttaaatccaccagacaaatttgccctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2212:SSA_2213|SSA_2212:SSA_2213:Possible polysaccharide transport protein, putative:Nucleotide sugar dehydratase, putative:<-<-:2214019..2214136 118 aatcttaggcaaaatcaagacaaccagagaagaaactattactgtcagcaaattggacaagacaacataggaaaaattagctattatttttttaaatccaccagacaaatttgccctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatcttaggcaaaatcaagacaaccagagaagaaactattactgtcagcaaattggacaagacaacataggaaaaattagctattatttttttaaatccaccagacaaatttgccctc Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 1 End: 108 I K P L I L V V L S S V I V T L L N S L V V Y S F N A I I K K F G G S M .......... aatcttaggcaaaatcaagacaaccagagaagaaactattactgtcagcaaattggacaagacaacataggaaaaattagctattatttttttaaatccaccagacaaatttgccctc 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================================================ aatcttaggcaaaatcaagacaaccagagaagaaactattactgtcagcaaattggacaagacaacataggaaaaattagctattatttttttaaatccaccagacaaatttgccctc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2212:SSA_2213|SSA_2212:SSA_2213:Possible polysaccharide transport protein, putative:Nucleotide sugar dehydratase, putative:<-<-:2214019..2214136 118 aatcttaggcaaaatcaagacaaccagagaagaaactattactgtcagcaaattggacaagacaacataggaaaaattagctattatttttttaaatccaccagacaaatttgccctc Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_009009_SSA_2212_SSA_2213|Possible polysaccharide transport protein, putative:Nucleotide sugar dehydratase, putative|NEGATIVE:NEGATIVE|[2214019,2214136]|118 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 aatcttaggcaaaatcaagacaaccagagaagaaactattactgtcagcaaattggacaagacaacataggaaaaattagctattannnnnnnaaatccaccagacaaatttgccctc aatcttaggcaaaatcaagacaaccagagaagaaactattactgtcagcaaattggacaagacaacataggaaaaattagctattatttttttaaatccaccagacaaatttgccctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUUAGGCAAAAUCAAGACAACCAGAGAAGAAACUAUUACUGUCAGCAAAUUGGACAAGACAACAUAGGAAAAAUUAGCUAUUAUUUUUUUAAAUCCACCAGACAAAUUUGCCCUC .......((((((.....((((.....((......)).....)))).......((((...(....)...((((((((........))))))))...)))).........))))))... (-14.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGGCAAAUUUGUCUGGUGGAUUUAAAAAAAUAAUAGCUAAUUUUUCCUAUGUUGUCUUGUCCAAUUUGCUGACAGUAAUAGUUUCUUCUCUGGUUGUCUUGAUUUUGCCUAAGAUU ..(((((((.(((((.((..((((....((.((((((..............)))))).))....))))..)))))))...(((........)))...........)))))))...... (-19.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 843 70 21 161 112 NC_009009:SSA_2212|5end_Possible_polysaccharide_transport_protein,_putative_2213928..2214158_NEGATIVE 271 55 16 88 44 NC_009009:SSA_2155|5end_hypothetical_protein_2156102..2156332_NEGATIVE 236 80 37 34 1 NC_009009:SSA_1549|5end_hypothetical_protein_1552112..1552342_NEGATIVE 235 48 5 230 191 NC_009009:SSA_1800|5end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1782371..1782601_NEGATIVE 218 57 21 79 36 NC_009009:SSA_2196|5end_Conserved_uncharacterized_protein_2197330..2197560_NEGATIVE 218 72 34 199 154 NC_009009:SSA_0141|5end_Copper_chaperone,_putative_136893..137123_POSITIVE 217 50 7 66 25 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 215 79 36 48 10 NC_009009:SSA_1671|5end_hypothetical_protein_1669304..1669534_POSITIVE 214 50 5 65 16 NC_009009:SSA_0879|5end_Cell_division_regulator,_negative_regulator_of_FtsZ_septation_ring_formation,_putative_873632..873862_POSITIVE 213 68 42 33 4 NC_009009:SSA_2282|5end_Phage_infection_protein,_putative_2285337..2285567_NEGATIVE 213 68 22 43 7 NC_009009:SSA_1103|5end_hypothetical_protein_1123833..1124063_POSITIVE 211 49 8 55 8 NC_009009:SSA_0510|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_508523..508753_POSITIVE 210 105 61 225 175 NC_009009:SSA_2289|5end_Cadmium_efflux_system_transcriptional_regulator_(ArsR-like),_putative_2291087..2291317_POSITIVE 210 105 61 225 175 NC_009009:SSA_2389|5end_Arsenical_resistance_operon_transcription_repressor,_putative_2032183..2032413_NEGATIVE 210 105 61 195 145 NC_009009:SSA_2387|5end_Arsenical_resistance_operon_transcription_repressor,_putative_2032213..2032443_NEGATIVE 208 72 32 230 192 NC_009009:SSA_2286|5end_Dihydroxy-acid_dehydratase,_putative_2289596..2289826_NEGATIVE 207 110 77 100 63 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 205 49 8 179 131 NC_009009:SSA_1501|5end_Cytidylate_kinase,_putative_1505772..1506002_NEGATIVE 205 82 42 152 120 NC_009009:SSA_0691|5end_D-ala,D-ala_ligase,_putative_675233..675463_POSITIVE 205 50 2 59 15 NC_009009:SSA_0603|5end_Cobalt_transporter,_putative_591596..591826_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 70 29 130 84 NC_009009:SSA_0390|3end_hypothetical_protein_385714..385864_POSITIVE 223 85 47 115 62 NC_009009:SSA_1317|3end_hypothetical_protein_1333398..1333548_NEGATIVE 218 57 21 95 52 NC_009009:SSA_2197|3end_hypothetical_protein_2197314..2197464_NEGATIVE 217 50 7 56 15 NC_009009:SSA_0238|3end_hypothetical_protein_233031..233181_POSITIVE 205 50 2 66 22 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 203 64 32 130 100 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 202 73 42 136 104 NC_009009:SSA_1800|3end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1781037..1781187_NEGATIVE 202 62 26 58 26 NC_009009:SSA_0822|3end_Large_conductance_mechano-sensitive_ion_channel,_putative_801589..801739_NEGATIVE 200 57 18 52 16 NC_009009:SSA_1753|3end_Transcriptional_regulator,_GntR_family_(repressor_of_trehalose_operon),_putative_1742740..1742890_POSITIVE 200 50 4 151 111 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 198 54 28 91 66 NC_009009:SSA_2056|3end_Cinnamoyl_ester_hydrolase,_putative_2059593..2059743_POSITIVE 196 81 42 50 1 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 192 83 41 65 6 NC_009009:SSA_1019|3end_Collagen-binding_surface_protein,_putative_1035377..1035527_POSITIVE 192 56 14 58 6 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE 192 48 5 72 21 NC_009009:SSA_0099|3end_hypothetical_protein_100134..100284_NEGATIVE 190 45 3 81 33 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 187 66 22 147 99 NC_009009:SSA_1828|3end_Glycerol_uptake_facilitator_protein,_putative_1818791..1818941_POSITIVE 187 67 41 151 130 NC_009009:SSA_0157|3end_hypothetical_protein_153877..154027_POSITIVE 186 38 8 50 18 NC_009009:SSA_1233|3end_Membrane_protein,_YqiH_family,_putative_1257626..1257776_POSITIVE 183 76 31 56 18 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE