Origin IGS: gtaaacgacaaattttcgattagcaaaactctgtcctcttttaaaaatcgcattaaaatctttttcgctcttgacgcgatagttttttctcaaaactcaactccatccaccaaaattatatctattataccatatttttcgaaaatgccaataagagccgctatgacgctgtttttgcaaatatttaaaaggttgattcaccaaaaaaacaccgcaatttccttgcgatgttccctatatctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagatatagggaacatcgcaaggaaattgcggtgtttttttggtgaatcaaccttttaaatatttgcaaaaacagcgtcatagcggctcttattggcattttcgaaaaatatggtataatagatataattttggtggatggagttgagttttgagaaaaaactatcgcgtcaagagcgaaaaagattttaatgcgatttttaaaagaggacagagttttgctaatcgaaaatttgtcgtttac Mask Tandem Repeat Region ================================================ gtaaacgacaaattttcgattagcaaaactctgtcctcttttaaaaatcgcattaaaatctttttcgctcttgacgcgatagttttttctcaaaactcaactccatccaccaaaattatatctattataccatatttttcgaaaatgccaataagagccgctatgacgctgtttttgcaaatatttaaaaggttgattcaccaaaaaaacaccgcaatttccttgcgatgttccctatatctta Find is-nt database================================================ Query_seq: SSA_2140:SSA_2141|SSA_2140:SSA_2141:Ribonuclease P protein component, putative:Argininosuccinate lyase, putative:<-<-:2140665..2140908 244 gtaaacgacaaattttcgattagcaaaactctgtcctcttttaaaaatcgcattaaaatctttttcgctcttgacgcgatagttttttctcaaaactcaactccatccaccaaaattatatctattataccatatttttcgaaaatgccaataagagccgctatgacgctgtttttgcaaatatttaaaaggttgattcaccaaaaaaacaccgcaatttccttgcgatgttccctatatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2140:SSA_2141|SSA_2140:SSA_2141:Ribonuclease P protein component, putative:Argininosuccinate lyase, putative:<-<-:2140665..2140908 244 gtaaacgacaaattttcgattagcaaaactctgtcctcttttaaaaatcgcattaaaatctttttcgctcttgacgcgatagttttttctcaaaactcaactccatccaccaaaattatatctattataccatatttttcgaaaatgccaataagagccgctatgacgctgtttttgcaaatatttaaaaggttgattcaccaaaaaaacaccgcaatttccttgcgatgttccctatatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2140:SSA_2141|SSA_2140:SSA_2141:Ribonuclease P protein component, putative:Argininosuccinate lyase, putative:<-<-:2140665..2140908 244 gtaaacgacaaattttcgattagcaaaactctgtcctcttttaaaaatcgcattaaaatctttttcgctcttgacgcgatagttttttctcaaaactcaactccatccaccaaaattatatctattataccatatttttcgaaaatgccaataagagccgctatgacgctgtttttgcaaatatttaaaaggttgattcaccaaaaaaacaccgcaatttccttgcgatgttccctatatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtaaacgacaaattttcgattagcaaaactctgtcctcttttaaaaatcgcattaaaatctttttcgctcttgacgcgatagttttttctcaaaactcaactccatccaccaaaattatatctattataccatatttttcgaaaatgccaataagagccgctatgacgctgtttttgcaaatatttaaaaggttgattcaccaaaaaaacaccgcaatttccttgcgatgttccctatatctta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 19 End: 243 .................. M S K T L S S F K N R I K I F F A L D A I V F S Q N S T P S T K I I S I I P Y F S K M P I R A A M T L F L Q I F K R L I . Protein_Len: 35 Strand: - Start: 100 End: 204 ................................................................................................... S W G G F N Y R N Y W I K R F H W Y S G S H R Q K Q L Y K F P Q N V M ........................................ Protein_Len: 35 Strand: - Start: 93 End: 197 ............................................................................................ F E V G D V L I I D I I G Y K E F I G I L A A I V S N K C I N L L N M ............................................... Protein_Len: 31 Strand: - Start: 1 End: 93 Y V V F K R N A F S Q G R K F I A N F D K E S K V R Y N K R M ....................................................................................................................................................... gtaaacgacaaattttcgattagcaaaactctgtcctcttttaaaaatcgcattaaaatctttttcgctcttgacgcgatagttttttctcaaaactcaactccatccaccaaaattatatctattataccatatttttcgaaaatgccaataagagccgctatgacgctgtttttgcaaatatttaaaaggttgattcaccaaaaaaacaccgcaatttccttgcgatgttccctatatctta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 115 End: 144 ..................................................................................................................TTTCGAAAAATATGGTATAATAGATATAAT.................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtaaacgacaaattttcgattagcaaaactctgtcctcttttaaaaatcgcattaaaatctttttcgctcttgacgcgatagttttttctcaaaactcaactccatccaccaaaattatatctattataccatatttttcgaaaatgccaataagagccgctatgacgctgtttttgcaaatatttaaaaggttgattcaccaaaaaaacaccgcaatttccttgcgatgttccctatatctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -2.2 Tail_Score: -3.15241 Start: 212 End: 228 Full_Region: TTCACCAAAAAAACA CCGCAA TTTCC TTGCGA TGTTCCCTATATCTT ...................................................................................................................................................................................................................CCGCAATTTCCTTGCGA................ Find igs database================================================ Query_seq: SSA_2140:SSA_2141|SSA_2140:SSA_2141:Ribonuclease P protein component, putative:Argininosuccinate lyase, putative:<-<-:2140665..2140908 244 gtaaacgacaaattttcgattagcaaaactctgtcctcttttaaaaatcgcattaaaatctttttcgctcttgacgcgatagttttttctcaaaactcaactccatccaccaaaattatatctattataccatatttttcgaaaatgccaataagagccgctatgacgctgtttttgcaaatatttaaaaggttgattcaccaaaaaaacaccgcaatttccttgcgatgttccctatatctta Intra-Species Hit: Count: 1 Min: 1 Max: 244 Len: 244 Subject: NC_009009_SSA_2140_SSA_2141|Ribonuclease P protein component, putative:Argininosuccinate lyase, putative|NEGATIVE:NEGATIVE|[2140665,2140908]|244 HSP 1 e-value: 1.0E-123 bit: 442.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1 Subject End: 244 gtaaacgacaaattttcgattagcaaaactctgtcctcttttaaaaatcgcattaaaatctttttcgctcttgacgcgatagttttttctcaaaactcaactccatccaccaaaattatatctattataccatatttttcgaaaatgccaataagagccgctatgacgctgtttttgcaaatatttaaaaggttgattcaccnnnnnnncaccgcaatttccttgcgatgttccctatatctta gtaaacgacaaattttcgattagcaaaactctgtcctcttttaaaaatcgcattaaaatctttttcgctcttgacgcgatagttttttctcaaaactcaactccatccaccaaaattatatctattataccatatttttcgaaaatgccaataagagccgctatgacgctgtttttgcaaatatttaaaaggttgattcaccaaaaaaacaccgcaatttccttgcgatgttccctatatctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAACGACAAAUUUUCGAUUAGCAAAACUCUGUCCUCUUUUAAAAAUCGCAUUAAAAUCUUUUUCGCUCUUGACGCGAUAGUUUUUUCUCAAAACUCAACUCCAUCCACCAAAAUUAUAUCUAUUAUACCAUAUUUUUCGAAAAUGCCAAUAAGAGCCGCUAUGACGCUGUUUUUGCAAAUAUUUAAAAGGUUGAUUCACCAAAAAAACACCGCAAUUUCCUUGCGAUGUUCCCUAUAUCUUA .....((((.........(((.(((((((..((((...((((((........))))))........(((((((..(((..((((((.....))))))...................((((.....))))................)))...)))))))......))))..).)))))).))).........))))............((((.(((((.....))))).))))............ (-32.47) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAUAUAGGGAACAUCGCAAGGAAAUUGCGGUGUUUUUUUGGUGAAUCAACCUUUUAAAUAUUUGCAAAAACAGCGUCAUAGCGGCUCUUAUUGGCAUUUUCGAAAAAUAUGGUAUAAUAGAUAUAAUUUUGGUGGAUGGAGUUGAGUUUUGAGAAAAAACUAUCGCGUCAAGAGCGAAAAAGAUUUUAAUGCGAUUUUUAAAAGAGGACAGAGUUUUGCUAAUCGAAAAUUUGUCGUUUAC ........((((((((((((((.....))))))))))))))..(((((.....((((((((...(((((......((......)).((((((.....((((..(.((((.((((..........)))).)))).)..))))..((..((((((.....))))))...))...))))))..............)))))..))))))))..((((((.(((((.....))))).)))))).))))) (-56.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 860 110 61 201 152 NC_009009:SSA_2140|5end_Ribonuclease_P_protein_component,_putative_2140574..2140804_NEGATIVE 306 175 141 80 36 NC_009009:SSA_1634|5end_Heme_utilization/adhesion_exoprotein,_putative_1637062..1637292_NEGATIVE 288 174 141 76 38 NC_009009:SSA_1573|5end_hypothetical_protein_1576536..1576766_NEGATIVE 286 109 63 211 153 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 282 228 189 49 11 NC_009009:SSA_1303|5end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322992..1323222_NEGATIVE 273 178 137 67 26 NC_009009:SSA_1122|5end_Thioredoxin_family_protein,_putative_1147871..1148101_POSITIVE 270 58 11 119 72 NC_009009:SSA_0603|5end_Cobalt_transporter,_putative_591596..591826_POSITIVE 262 142 103 135 88 NC_009009:SSA_1802|5end_Snf2_family_protein,_putative_1786470..1786700_NEGATIVE 261 66 23 70 24 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 261 170 132 215 173 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 260 186 151 81 52 NC_009009:SSA_0753|5end_Foldase_protein_prsA_precursor,_putative_734968..735198_POSITIVE 259 178 135 190 154 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 257 199 151 182 113 NC_009009:SSA_0691|5end_D-ala,D-ala_ligase,_putative_675233..675463_POSITIVE 256 199 154 184 134 NC_009009:SSA_2083|5end_hypothetical_protein_2087969..2088199_NEGATIVE 255 179 133 230 182 NC_009009:SSA_0325|5end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_317603..317833_POSITIVE 252 170 127 55 9 NC_009009:SSA_1296|5end_hypothetical_protein_1313013..1313243_NEGATIVE 251 160 116 162 117 NC_009009:SSA_0845|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_830046..830276_NEGATIVE 251 39 13 198 165 NC_009009:SSA_0094|5end_Cell_wall_metabolism,_LysM_type_protein,_putative_95345..95575_POSITIVE 251 89 48 128 86 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 250 177 131 43 7 NC_009009:SSA_0573|5end_hypothetical_protein_568732..568962_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 178 146 146 109 NC_009009:SSA_2068|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_2070931..2071081_NEGATIVE 273 178 137 52 11 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 270 58 11 126 79 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 255 179 133 140 92 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 254 234 210 125 105 NC_009009:SSA_1315|3end_hypothetical_protein_1331408..1331558_NEGATIVE 252 174 147 53 28 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 251 89 48 120 78 NC_009009:SSA_0089|3end_V-type_sodium_ATPase,_subunit_F,_putative_90330..90480_POSITIVE 250 227 181 59 13 NC_009009:SSA_0287|3end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_280702..280852_POSITIVE 249 178 137 46 3 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 249 108 61 133 77 NC_009009:SSA_0809|3end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791606..791756_POSITIVE 248 178 135 90 49 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE 246 108 70 109 66 NC_009009:SSA_0200|3end_Bifunctional_folate_synthesis_protein,_putative_199810..199960_POSITIVE 244 112 75 145 103 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 242 170 122 80 32 NC_009009:SSA_0931|3end_hypothetical_protein_941335..941485_POSITIVE 242 78 32 139 96 NC_009009:SSA_0221|3end_PTS_system,_mannose-specific_IIC_component,_putative_217295..217445_POSITIVE 241 232 191 48 10 NC_009009:SSA_1933|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase,_putative_1920893..1921043_NEGATIVE 240 178 135 145 103 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 239 236 194 116 82 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 239 169 145 28 1 NC_009009:SSA_0066|3end_hypothetical_protein_68095..68245_POSITIVE 237 106 67 89 49 NC_009009:SSA_1011|3end_hypothetical_protein_1014804..1014954_POSITIVE