Origin IGS: gatcttattcctttccagagtgttttttgcataccgtactattatactacaaattcgggcttttggggcaaaagtttgcagaaaaatttgttataatggaggaggtttataagtgaaacgaggtcaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttgacctcgtttcacttataaacctcctccattataacaaatttttctgcaaacttttgccccaaaagcccgaatttgtagtataatagtacggtatgcaaaaaacactctggaaaggaataagatc Mask Tandem Repeat Region ================================================ gatcttattcctttccagagtgttttttgcataccgtactattatactacaaattcgggcttttggggcaaaagtttgcagaaaaatttgttataatggaggaggtttataagtgaaacgaggtcaag Find is-nt database================================================ Query_seq: SSA_0447:SSA_0448|SSA_0447:SSA_0448:Magnesium and cobalt transporter, putative:Excinuclease ATPase subunit A, putative:<-->:446492..446619 128 gatcttattcctttccagagtgttttttgcataccgtactattatactacaaattcgggcttttggggcaaaagtttgcagaaaaatttgttataatggaggaggtttataagtgaaacgaggtcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0447:SSA_0448|SSA_0447:SSA_0448:Magnesium and cobalt transporter, putative:Excinuclease ATPase subunit A, putative:<-->:446492..446619 128 gatcttattcctttccagagtgttttttgcataccgtactattatactacaaattcgggcttttggggcaaaagtttgcagaaaaatttgttataatggaggaggtttataagtgaaacgaggtcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0447:SSA_0448|SSA_0447:SSA_0448:Magnesium and cobalt transporter, putative:Excinuclease ATPase subunit A, putative:<-->:446492..446619 128 gatcttattcctttccagagtgttttttgcataccgtactattatactacaaattcgggcttttggggcaaaagtttgcagaaaaatttgttataatggaggaggtttataagtgaaacgaggtcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatcttattcctttccagagtgttttttgcataccgtactattatactacaaattcgggcttttggggcaaaagtttgcagaaaaatttgttataatggaggaggtttataagtgaaacgaggtcaag Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 2 End: 109 . M L F L S R V F F A Y R T I I L Q I R A F G A K V C R K I C Y N G G G L ................... gatcttattcctttccagagtgttttttgcataccgtactattatactacaaattcgggcttttggggcaaaagtttgcagaaaaatttgttataatggaggaggtttataagtgaaacgaggtcaag 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================================================ gatcttattcctttccagagtgttttttgcataccgtactattatactacaaattcgggcttttggggcaaaagtttgcagaaaaatttgttataatggaggaggtttataagtgaaacgaggtcaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0447:SSA_0448|SSA_0447:SSA_0448:Magnesium and cobalt transporter, putative:Excinuclease ATPase subunit A, putative:<-->:446492..446619 128 gatcttattcctttccagagtgttttttgcataccgtactattatactacaaattcgggcttttggggcaaaagtttgcagaaaaatttgttataatggaggaggtttataagtgaaacgaggtcaag Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_009009_SSA_0447_SSA_0448|Magnesium and cobalt transporter, putative:Excinuclease ATPase subunit A, putative|NEGATIVE:POSITIVE|[446492,446619]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 gatcttattcctttccagagtgttttttgcataccgtactattatactacaaattcgggcttttggggcaaaagtttgcagaaaaatttgttataatggaggaggtttataagtgaaacgaggtcaag gatcttattcctttccagagtgttttttgcataccgtactattatactacaaattcgggcttttggggcaaaagtttgcagaaaaatttgttataatggaggaggtttataagtgaaacgaggtcaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUCUUAUUCCUUUCCAGAGUGUUUUUUGCAUACCGUACUAUUAUACUACAAAUUCGGGCUUUUGGGGCAAAAGUUUGCAGAAAAAUUUGUUAUAAUGGAGGAGGUUUAUAAGUGAAACGAGGUCAAG ((((((.((((((.((...((((.....)))).((...((((((((..(((((((((((((((((...))))))))))......))))))))))))))).)).)).....))).)))..))))))... (-28.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGACCUCGUUUCACUUAUAAACCUCCUCCAUUAUAACAAAUUUUUCUGCAAACUUUUGCCCCAAAAGCCCGAAUUUGUAGUAUAAUAGUACGGUAUGCAAAAAACACUCUGGAAAGGAAUAAGAUC ...............(((((...(((..((((.....((((((((..((((((....))))......))...)))))))).((((....))))..................)))).))).)))))... (-15.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 855 80 31 171 122 NC_009009:SSA_0447|5end_Magnesium_and_cobalt_transporter,_putative_446401..446631_NEGATIVE 333 55 11 184 137 NC_009009:SSA_1623|5end_50S_ribosomal_protein_L11,_putative_1625968..1626198_NEGATIVE 271 59 11 145 107 NC_009009:SSA_1494|5end_Conserved_uncharacterized_protein_1500773..1501003_NEGATIVE 270 84 58 36 9 NC_009009:SSA_0071|5end_N-acetylmannosamine-6-p_hosphate_2-epimerase_1,_putative_75210..75440_POSITIVE 259 48 3 168 125 NC_009009:SSA_2301|5end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2303268..2303498_NEGATIVE 257 99 56 94 50 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 254 51 16 109 70 NC_009009:SSA_1075|5end_Coproporphyrinogen_III_oxidase,_putative_1093093..1093323_POSITIVE 250 118 75 153 113 NC_009009:SSA_1762|5end_Permease,_putative_1750052..1750282_NEGATIVE 244 78 33 221 181 NC_009009:SSA_2014|5end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014807..2015037_NEGATIVE 243 98 55 215 172 NC_009009:SSA_1825|5end_hypothetical_protein_1812951..1813181_POSITIVE 238 76 34 223 187 NC_009009:SSA_0292|5end_Transcriptional_regulator,_AraC_family_(arabinose_operon_control),_putative_286208..286438_POSITIVE 237 79 34 68 27 NC_009009:SSA_2259|5end_hypothetical_protein_2255422..2255652_NEGATIVE 228 48 7 94 48 NC_009009:SSA_2316|5end_General_secretory_pathway_protein_F,_putative_2318342..2318572_NEGATIVE 226 120 93 189 165 NC_009009:SSA_1503|5end_Ferredoxin,_putative_1506209..1506439_POSITIVE 226 100 53 97 56 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 225 79 50 196 159 NC_009009:SSA_0928|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_936679..936909_POSITIVE 224 50 8 136 96 NC_009009:SSA_1510|5end_Rhamnosyltransferase,_putative_1515336..1515566_NEGATIVE 223 79 38 79 47 NC_009009:SSA_0903|5end_NAD(P)H_dehydrogenase_(quinone),_putative_893242..893472_POSITIVE 222 107 67 205 161 NC_009009:SSA_1247|5end_hypothetical_protein_1272358..1272588_NEGATIVE 220 77 33 76 35 NC_009009:SSA_1103|5end_hypothetical_protein_1123833..1124063_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 68 38 49 16 NC_009009:SSA_0865|3end_hypothetical_protein_856850..857000_POSITIVE 259 48 3 132 89 NC_009009:SSA_2302|3end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2303304..2303454_NEGATIVE 257 99 56 89 45 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 242 70 28 41 5 NC_009009:SSA_0392|3end_hypothetical_protein_388303..388453_POSITIVE 232 83 44 150 113 NC_009009:SSA_1041|3end_Sugar_ABC_transporter,_permease_protein,_putative_1057434..1057584_POSITIVE 228 48 7 90 44 NC_009009:SSA_2317|3end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2318346..2318496_NEGATIVE 226 100 53 69 28 NC_009009:SSA_0220|3end_PTS_system,_mannose-specific_IIB_component,_putative_216422..216572_POSITIVE 217 100 52 61 13 NC_009009:SSA_1401|3end_Transcriptional_regulator_GntR_family_1414461..1414611_POSITIVE 217 79 31 141 98 NC_009009:SSA_0226|3end_60_kDa_chaperonin_220649..220799_POSITIVE 216 30 1 121 88 NC_009009:SSA_1399|3end_hypothetical_protein_1411659..1411809_NEGATIVE 215 49 2 149 100 NC_009009:SSA_0346|3end_hypothetical_protein_340322..340472_POSITIVE 212 107 63 86 19 NC_009009:SSA_2391|3end_30S_ribosomal_protein_S14,_putative_114517..114667_POSITIVE 211 92 58 34 2 NC_009009:SSA_0939|3end_Inositol_monophosphatase_(Mg++_dependent),_putative_947705..947855_POSITIVE 210 79 35 66 27 NC_009009:SSA_0227|3end_Collagen-binding_surface_protein,_putative_222970..223120_POSITIVE 206 58 12 94 48 NC_009009:SSA_2246|3end_Competence-damage_protein,_putative_2241168..2241318_NEGATIVE 206 66 24 94 50 NC_009009:SSA_1441|3end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1444839..1444989_NEGATIVE 204 79 32 141 92 NC_009009:SSA_1740|3end_hypothetical_protein_1727081..1727231_NEGATIVE 204 92 56 137 104 NC_009009:SSA_1571|3end_Threonyl-tRNA_synthetase,_putative_1573211..1573361_NEGATIVE 204 78 33 88 42 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 204 68 30 98 53 NC_009009:SSA_0790|3end_hypothetical_protein_773357..773507_POSITIVE