Origin IGS: tggggtgaatatggggtgaattttggggtgaactttgattttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcaatacgattatatcaacgtttacagacattcaagaattatttcttggatgtcttttttgtttcaaaaaatcaaagttcaccccaaaattcaccccatattcacccca Mask Tandem Repeat Region ================================================ tggggtgaatatggggtgaattttggggtgaactttgattttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga Find is-nt database================================================ Query_seq: SSA_2032:SSA_2033|SSA_2032:SSA_2033:Integrase/recombinase, phage integrase family, putative:30S ribosomal protein S9, putative:-><-:2038368..2038476 109 tggggtgaatatggggtgaattttggggtgaactttgattttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2032:SSA_2033|SSA_2032:SSA_2033:Integrase/recombinase, phage integrase family, putative:30S ribosomal protein S9, putative:-><-:2038368..2038476 109 tggggtgaatatggggtgaattttggggtgaactttgattttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2032:SSA_2033|SSA_2032:SSA_2033:Integrase/recombinase, phage integrase family, putative:30S ribosomal protein S9, putative:-><-:2038368..2038476 109 tggggtgaatatggggtgaattttggggtgaactttgattttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggggtgaatatggggtgaattttggggtgaactttgattttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 3 End: 101 .. P S Y P T F K P T F K S K K F C F L C G L F L E Q I D T F T S I M ........ Protein_Len: 35 Strand: - Start: 2 End: 106 . P H I H P S N Q P S S Q N K S V F F V D L F Y N K F T Q L R Q Y L R M ... Protein_Len: 32 Strand: - Start: 1 End: 96 P T F I P H I K P H V K I K Q F L F S M W S I I R S H R Y V N M ............. tggggtgaatatggggtgaattttggggtgaactttgattttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga 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================================================ tggggtgaatatggggtgaattttggggtgaactttgattttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2032:SSA_2033|SSA_2032:SSA_2033:Integrase/recombinase, phage integrase family, putative:30S ribosomal protein S9, putative:-><-:2038368..2038476 109 tggggtgaatatggggtgaattttggggtgaactttgattttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_009009_SSA_2032_SSA_2033|Integrase/recombinase, phage integrase family, putative:30S ribosomal protein S9, putative|POSITIVE:NEGATIVE|[2038368,2038476]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 tggggtgaatatggggtgaattttggggtgaactttgattttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga tggggtgaatatggggtgaattttggggtgaactttgattttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga Inter-species Hit: Count: 3 Min: 3 Max: 109 Len: 107 Subject: NC_008532_STER_0128_STER_0130|Ribosomal protein S9:hypothetical protein|POSITIVE:POSITIVE|[105273,106259]|987 HSP 1 e-value: 3.0E-19 bit: 95.6 Len: 107 Query Start:3 Query End:109 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 108 ..gggtgaatatggggtgaattttggggtgaactttgattttttgaa-acaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga ..gggtgaacatggggtgaattttggggtgaactttataaatttcaacaaaaaaaagacatccaagataaaaatcttgaatgtcttgaaacgttgatataatcgtattga Subject: NC_006449_str0094_str0095|30S ribosomal protein S9:Integrase/recombinase, putative, truncated|POSITIVE:NEGATIVE|[102357,102512]|156 HSP 1 e-value: 1.0E-18 bit: 93.7 Len: 107 Query Start:3 Query End:109 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 107 ..gggtgaatatggggtgaattttggggtgaactttgattttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga ..gggtgaacatggggtgaattttggggtgaactttataaatttcaacaaaaaaagacacccaagataaaaatcttgaatgtcttgaaacgttgatataatcgtattga Subject: NC_006448_stu0094_stu0095|30S ribosomal protein S9:Integrase/recombinase, putative, truncated|POSITIVE:NEGATIVE|[103575,103733]|159 HSP 1 e-value: 7.0E-17 bit: 87.7 Len: 107 Query Start:3 Query End:109 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 110 ..gggtgaatatggggtgaattttggggtgaactttg---attttttgaaacaaaaaagacatccaagaaataattcttgaatgtctgtaaacgttgatataatcgtattga ..gggtgaacatggggtgaattttgggatgaactttataaatttcaacaaaaaaaaaagacatccaagataaaaatcttgaatgtcttgaaacgttgatataatcgtattga Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGUGAAUAUGGGGUGAAUUUUGGGGUGAACUUUGAUUUUUUGAAACAAAAAAGACAUCCAAGAAAUAAUUCUUGAAUGUCUGUAAACGUUGAUAUAAUCGUAUUGA .....(((((((...(((..(..(((....)))..)..)))...(((.....((((((.((((((....)))))).))))))......))).......))))))).. (-21.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAUACGAUUAUAUCAACGUUUACAGACAUUCAAGAAUUAUUUCUUGGAUGUCUUUUUUGUUUCAAAAAAUCAAAGUUCACCCCAAAAUUCACCCCAUAUUCACCC .......((((.....((((.....(((((((((((((....)))))))))))))....))))......)))).................................. (-19.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 60 12 214 168 NC_009009:SSA_1189|5end_GTP-binding_protein,_putative_1217657..1217887_NEGATIVE 232 50 1 189 130 NC_009009:SSA_1692|5end_Phospho-B-galactosidase_LacG,_putative_1685006..1685236_NEGATIVE 231 44 2 81 45 NC_009009:SSA_2032|5end_Integrase/recombinase,_phage_integrase_family,_putative_2038006..2038236_POSITIVE 210 84 53 175 141 NC_009009:SSA_0176|5end_DNA-directed_RNA_polymerase_I,_beta_chain_(140_kDa_subunit),_putative_174981..175211_POSITIVE 204 93 54 215 182 NC_009009:SSA_1096|5end_Methyltransferase,_putative_1113072..1113302_POSITIVE 204 44 1 209 169 NC_009009:SSA_0244|5end_hypothetical_protein_238698..238928_POSITIVE 199 28 1 166 136 NC_009009:SSA_1238|5end_hypothetical_protein_1263154..1263384_NEGATIVE 196 60 12 213 168 NC_009009:SSA_1622|5end_50S_ribosomal_protein_L1,_putative_1625441..1625671_NEGATIVE 193 38 10 164 140 NC_009009:SSA_2038|5end_hypothetical_protein_2041627..2041857_POSITIVE 190 57 17 218 168 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 190 42 1 102 61 NC_009009:SSA_1011|5end_hypothetical_protein_1014134..1014364_POSITIVE 190 44 1 135 86 NC_009009:SSA_0293|5end_hypothetical_protein_287613..287843_NEGATIVE 190 29 2 164 132 NC_009009:SSA_0132|5end_DNA-directed_RNA_polymerase,_alpha_chain,_putative_121146..121376_POSITIVE 189 37 11 213 188 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 186 91 54 85 48 NC_009009:SSA_2076|5end_Conserved_uncharacterized_protein_2080481..2080711_NEGATIVE 186 44 2 80 32 NC_009009:SSA_1480|5end_hypothetical_protein_1484811..1485041_NEGATIVE 182 27 1 231 212 NC_009009:SSA_0054|5end_Phosphotransferase_system_sugar-specific_EIIB_component,_putative_58532..58762_POSITIVE 181 42 7 125 90 NC_009009:SSA_1250|5end_Conserved_uncharacterized_protein,_putative_1274512..1274742_NEGATIVE 181 100 60 190 144 NC_009009:SSA_0824|5end_DNA_primase_(bacterial_type),_putative_802053..802283_POSITIVE 179 94 72 130 104 NC_009009:SSA_0247|5end_hypothetical_protein_240032..240262_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 60 12 72 26 NC_009009:SSA_1190|3end_Conserved_uncharacterized_protein_1217799..1217949_NEGATIVE 232 50 1 90 31 NC_009009:SSA_1693|3end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1685105..1685255_NEGATIVE 230 42 11 40 13 NC_009009:SSA_0799|3end_hypothetical_protein_781713..781863_NEGATIVE 208 44 11 150 109 NC_009009:SSA_0173|3end_23S_rRNA_m1G745_methyltransferase,_putative_169696..169846_NEGATIVE 204 93 54 151 118 NC_009009:SSA_1095|3end_Peptidoglycan_hydrolase,_putative_1113088..1113238_POSITIVE 196 60 12 111 66 NC_009009:SSA_1623|3end_50S_ribosomal_protein_L11,_putative_1625543..1625693_NEGATIVE 194 48 1 134 68 NC_009009:SSA_2129|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_2132223..2132373_NEGATIVE 194 82 53 36 7 NC_009009:SSA_2032|3end_Integrase/recombinase,_phage_integrase_family,_putative_2038307..2038457_POSITIVE 190 29 2 118 86 NC_009009:SSA_0131|3end_30S_ribosomal_protein_S11,_putative_121180..121330_POSITIVE 186 44 2 65 17 NC_009009:SSA_1481|3end_FmtA-like_protein,_putative_1484826..1484976_NEGATIVE 186 36 10 128 99 NC_009009:SSA_0743|3end_Transcriptional_repressor_(arginine_synthesis),_putative_725289..725439_NEGATIVE 184 65 21 64 22 NC_009009:SSA_2109|3end_Elongation_factor_G,_putative_2112787..2112937_NEGATIVE 181 42 7 144 109 NC_009009:SSA_1251|3end_Hydrolase,_HD_superfamily,_putative_1274493..1274643_NEGATIVE 181 85 55 125 93 NC_009009:SSA_0095|3end_Threonine_synthase,_putative_98119..98269_POSITIVE 179 64 21 80 39 NC_009009:SSA_0362|3end_Thioredoxin,_putative_353594..353744_POSITIVE 179 94 72 124 98 NC_009009:SSA_0246|3end_Conserved_uncharacterized_protein_240106..240256_POSITIVE 177 46 2 70 23 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 177 44 8 127 92 NC_009009:SSA_0813|3end_Thioredoxin_reductase,_putative_794438..794588_NEGATIVE 175 65 21 67 33 NC_009009:SSA_2185|3end_Adenylosuccinate_synthetase,_putative_2183998..2184148_NEGATIVE 175 44 10 85 42 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE