Origin IGS: acagttctcctacttttctagcttattctcattatagcataaccatctgtcttttctctatttttcccctgctcttcttatctatcctatactctctatcttaaaagaaacgaaaaaagaaccagtcttctagccagttccttttggtattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaataccaaaaggaactggctagaagactggttcttttttcgtttcttttaagatagagagtataggatagataagaagagcaggggaaaaatagagaaaagacagatggttatgctataatgagaataagctagaaaagtaggagaactgt Mask Tandem Repeat Region ================================================ acagttctcctacttttctagcttattctcattatagcataaccatctgtcttttctctatttttcccctgctcttcttatctatcctatactctctatcttaaaagaaacgaaaaaagaaccagtcttctagccagttccttttggtattta Find is-nt database================================================ Query_seq: SSA_1795:SSA_1796|SSA_1795:SSA_1796:Guanosine 3',5'-bis-pyrophosphate (ppGpp) synthetase, putative:Transcription elongation factor GreA, putative:<-<-:1777762..1777914 153 acagttctcctacttttctagcttattctcattatagcataaccatctgtcttttctctatttttcccctgctcttcttatctatcctatactctctatcttaaaagaaacgaaaaaagaaccagtcttctagccagttccttttggtattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1795:SSA_1796|SSA_1795:SSA_1796:Guanosine 3',5'-bis-pyrophosphate (ppGpp) synthetase, putative:Transcription elongation factor GreA, putative:<-<-:1777762..1777914 153 acagttctcctacttttctagcttattctcattatagcataaccatctgtcttttctctatttttcccctgctcttcttatctatcctatactctctatcttaaaagaaacgaaaaaagaaccagtcttctagccagttccttttggtattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1795:SSA_1796|SSA_1795:SSA_1796:Guanosine 3',5'-bis-pyrophosphate (ppGpp) synthetase, putative:Transcription elongation factor GreA, putative:<-<-:1777762..1777914 153 acagttctcctacttttctagcttattctcattatagcataaccatctgtcttttctctatttttcccctgctcttcttatctatcctatactctctatcttaaaagaaacgaaaaaagaaccagtcttctagccagttccttttggtattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acagttctcctacttttctagcttattctcattatagcataaccatctgtcttttctctatttttcccctgctcttcttatctatcctatactctctatcttaaaagaaacgaaaaaagaaccagtcttctagccagttccttttggtattta Predict ORF larger than 30AA ================================================ acagttctcctacttttctagcttattctcattatagcataaccatctgtcttttctctatttttcccctgctcttcttatctatcctatactctctatcttaaaagaaacgaaaaaagaaccagtcttctagccagttccttttggtattta 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================================================ acagttctcctacttttctagcttattctcattatagcataaccatctgtcttttctctatttttcccctgctcttcttatctatcctatactctctatcttaaaagaaacgaaaaaagaaccagtcttctagccagttccttttggtattta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1795:SSA_1796|SSA_1795:SSA_1796:Guanosine 3',5'-bis-pyrophosphate (ppGpp) synthetase, putative:Transcription elongation factor GreA, putative:<-<-:1777762..1777914 153 acagttctcctacttttctagcttattctcattatagcataaccatctgtcttttctctatttttcccctgctcttcttatctatcctatactctctatcttaaaagaaacgaaaaaagaaccagtcttctagccagttccttttggtattta Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: NC_009009_SSA_1795_SSA_1796|Guanosine 3',5'-bis-pyrophosphate (ppGpp) synthetase, putative:Transcription elongation factor GreA, putative|NEGATIVE:NEGATIVE|[1777762,1777914]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 acagttctcctacttttctagcttattctcattatagcataaccatctgtcttttctctatttttcccctgctcttcttatctatcctatactctctatcttaaaagaaacgaaaaaagaaccagtcttctagccagttccttttggtattta acagttctcctacttttctagcttattctcattatagcataaccatctgtcttttctctatttttcccctgctcttcttatctatcctatactctctatcttaaaagaaacgaaaaaagaaccagtcttctagccagttccttttggtattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGUUCUCCUACUUUUCUAGCUUAUUCUCAUUAUAGCAUAACCAUCUGUCUUUUCUCUAUUUUUCCCCUGCUCUUCUUAUCUAUCCUAUACUCUCUAUCUUAAAAGAAACGAAAAAAGAACCAGUCUUCUAGCCAGUUCCUUUUGGUAUUUA ...(((((.....(((((..(((............)))............................................................(((....)))...))))).)))))..........(((((......)))))..... (-11.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUACCAAAAGGAACUGGCUAGAAGACUGGUUCUUUUUUCGUUUCUUUUAAGAUAGAGAGUAUAGGAUAGAUAAGAAGAGCAGGGGAAAAAUAGAGAAAAGACAGAUGGUUAUGCUAUAAUGAGAAUAAGCUAGAAAAGUAGGAGAACUGU ......((....))..((((((......((.(((((((((((..((((((......)))))).........)).))))))))).)).....................((((.....))))..........)))))).....(((.....))). (-22.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 843 90 41 181 132 NC_009009:SSA_1795|5end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777671..1777901_NEGATIVE 327 75 36 128 81 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 304 87 41 53 5 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 295 97 51 155 100 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 294 87 46 97 49 NC_009009:SSA_1702|5end_hypothetical_protein_1693462..1693692_NEGATIVE 294 147 124 47 24 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 291 123 84 214 174 NC_009009:SSA_1189|5end_GTP-binding_protein,_putative_1217657..1217887_NEGATIVE 290 49 1 141 88 NC_009009:SSA_0874|5end_hypothetical_protein_867935..868165_POSITIVE 287 49 7 60 17 NC_009009:SSA_0616|5end_YlbN-like_protein,_putative_609245..609475_POSITIVE 284 100 53 147 97 NC_009009:SSA_1327|5end_hypothetical_protein_1344301..1344531_NEGATIVE 282 80 40 140 85 NC_009009:SSA_0283|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIB_component,_putative_274559..274789_POSITIVE 279 69 27 168 116 NC_009009:SSA_1354|5end_hypothetical_protein_1369052..1369282_NEGATIVE 273 87 45 113 79 NC_009009:SSA_1103|5end_hypothetical_protein_1123833..1124063_POSITIVE 271 80 37 147 104 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 271 77 42 130 87 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 267 76 32 107 58 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 266 148 123 173 152 NC_009009:SSA_1130|5end_Iron-dependent_peroxidase,_putative_1155802..1156032_POSITIVE 264 78 42 99 58 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 260 78 36 175 118 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 259 83 43 127 85 NC_009009:SSA_0467|5end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_470588..470818_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 75 36 141 94 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 295 97 51 77 22 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 291 123 84 72 32 NC_009009:SSA_1190|3end_Conserved_uncharacterized_protein_1217799..1217949_NEGATIVE 284 100 53 106 56 NC_009009:SSA_1328|3end_hypothetical_protein_1344342..1344492_NEGATIVE 284 88 46 137 90 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 282 80 40 119 64 NC_009009:SSA_0282|3end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIA_component,_putative_274618..274768_POSITIVE 279 69 27 137 85 NC_009009:SSA_1355|3end_hypothetical_protein_1369083..1369233_NEGATIVE 277 145 108 92 49 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 276 87 43 148 96 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 267 76 32 106 57 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 259 83 43 127 85 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 258 72 31 119 75 NC_009009:SSA_0992|3end_hypothetical_protein_994147..994297_POSITIVE 254 82 42 47 11 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 253 70 21 136 83 NC_009009:SSA_1324|3end_Ceramide_glucosyltransferase,_putative_1340428..1340578_NEGATIVE 252 96 51 105 46 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 251 150 106 91 52 NC_009009:SSA_1032|3end_30S_ribosomal_protein_subunit_S20,_putative_1048313..1048463_NEGATIVE 251 104 62 122 74 NC_009009:SSA_0809|3end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791606..791756_POSITIVE 247 59 13 109 72 NC_009009:SSA_1972|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1967811..1967961_NEGATIVE 247 83 41 122 84 NC_009009:SSA_1490|3end_Ribonuclease_BN,_putative_1495821..1495971_NEGATIVE 247 88 46 138 95 NC_009009:SSA_0511|3end_Propanediol_utilization_kinase,_putative_510556..510706_POSITIVE