Origin IGS: atcaacgaccacaaaatagctgaaataatctaatttttttggtaaaataaaaggtagcaatctaaagcctattgaaatataaatttcatggagcattagattatagaaatgacacaaaaagaggacggtccaactc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagttggaccgtcctctttttgtgtcatttctataatctaatgctccatgaaatttatatttcaataggctttagattgctaccttttattttaccaaaaaaattagattatttcagctattttgtggtcgttgat Mask Tandem Repeat Region ================================================ atcaacgaccacaaaatagctgaaataatctaatttttttggtaaaataaaaggtagcaatctaaagcctattgaaatataaatttcatggagcattagattatagaaatgacacaaaaagaggacggtccaactc Find is-nt database================================================ Query_seq: SSA_1211:SSA_1212|SSA_1211:SSA_1212:hypothetical protein:Ribose-phosphate pyrophosphokinase 2, putative:->->:1235405..1235540 136 atcaacgaccacaaaatagctgaaataatctaatttttttggtaaaataaaaggtagcaatctaaagcctattgaaatataaatttcatggagcattagattatagaaatgacacaaaaagaggacggtccaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1211:SSA_1212|SSA_1211:SSA_1212:hypothetical protein:Ribose-phosphate pyrophosphokinase 2, putative:->->:1235405..1235540 136 atcaacgaccacaaaatagctgaaataatctaatttttttggtaaaataaaaggtagcaatctaaagcctattgaaatataaatttcatggagcattagattatagaaatgacacaaaaagaggacggtccaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1211:SSA_1212|SSA_1211:SSA_1212:hypothetical protein:Ribose-phosphate pyrophosphokinase 2, putative:->->:1235405..1235540 136 atcaacgaccacaaaatagctgaaataatctaatttttttggtaaaataaaaggtagcaatctaaagcctattgaaatataaatttcatggagcattagattatagaaatgacacaaaaagaggacggtccaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcaacgaccacaaaatagctgaaataatctaatttttttggtaaaataaaaggtagcaatctaaagcctattgaaatataaatttcatggagcattagattatagaaatgacacaaaaagaggacggtccaactc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 1 End: 117 D V V V F Y S F Y D L K K P L I F P L L R F G I S I Y I E H L M L N Y F H C M ................... atcaacgaccacaaaatagctgaaataatctaatttttttggtaaaataaaaggtagcaatctaaagcctattgaaatataaatttcatggagcattagattatagaaatgacacaaaaagaggacggtccaactc 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: 83 Start: 19 End: 48 ..................GCTGAAATAATCTAATTTTTTTGGTAAAAT........................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcaacgaccacaaaatagctgaaataatctaatttttttggtaaaataaaaggtagcaatctaaagcctattgaaatataaatttcatggagcattagattatagaaatgacacaaaaagaggacggtccaactc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1211:SSA_1212|SSA_1211:SSA_1212:hypothetical protein:Ribose-phosphate pyrophosphokinase 2, putative:->->:1235405..1235540 136 atcaacgaccacaaaatagctgaaataatctaatttttttggtaaaataaaaggtagcaatctaaagcctattgaaatataaatttcatggagcattagattatagaaatgacacaaaaagaggacggtccaactc Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: NC_009009_SSA_1211_SSA_1212|hypothetical protein:Ribose-phosphate pyrophosphokinase 2, putative|POSITIVE:POSITIVE|[1235405,1235540]|136 HSP 1 e-value: 4.0E-59 bit: 228.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 atcaacgaccacaaaatagctgaaataatctaannnnnnnggtaaaataaaaggtagcaatctaaagcctattgaaatataaatttcatggagcattagattatagaaatgacacaaaaagaggacggtccaactc atcaacgaccacaaaatagctgaaataatctaatttttttggtaaaataaaaggtagcaatctaaagcctattgaaatataaatttcatggagcattagattatagaaatgacacaaaaagaggacggtccaactc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAACGACCACAAAAUAGCUGAAAUAAUCUAAUUUUUUUGGUAAAAUAAAAGGUAGCAAUCUAAAGCCUAUUGAAAUAUAAAUUUCAUGGAGCAUUAGAUUAUAGAAAUGACACAAAAAGAGGACGGUCCAACUC ......((((......(((.(......).))).((((((((.................(((((((.((((((.(((((....))))))))).)).))))))).((....))...))))))))....))))...... (-22.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUUGGACCGUCCUCUUUUUGUGUCAUUUCUAUAAUCUAAUGCUCCAUGAAAUUUAUAUUUCAAUAGGCUUUAGAUUGCUACCUUUUAUUUUACCAAAAAAAUUAGAUUAUUUCAGCUAUUUUGUGGUCGUUGAU (((...(((((.........)).)))..)))..((((((((.(((...((((((....))))))...))).))))))))..............((((...(((.(((..........))).))).))))....... (-21.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 214 70 40 173 142 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 212 97 56 190 147 NC_009009:SSA_2346|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2348546..2348776_NEGATIVE 209 130 83 70 30 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 204 88 50 142 109 NC_009009:SSA_1515|5end_hypothetical_protein_1522129..1522359_NEGATIVE 204 28 4 47 21 NC_009009:SSA_0960|5end_Sensor_protein_ciaH,_putative_968506..968736_POSITIVE 204 98 51 90 39 NC_009009:SSA_0375|5end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_364257..364487_POSITIVE 202 104 78 196 165 NC_009009:SSA_1765|5end_Conserved_uncharacterized_protein_1753036..1753266_POSITIVE 200 125 88 205 164 NC_009009:SSA_1916|5end_hypothetical_protein_1905487..1905717_POSITIVE 198 71 37 69 36 NC_009009:SSA_1730|5end_hypothetical_protein_1716057..1716287_NEGATIVE 197 130 84 157 102 NC_009009:SSA_0398|5end_hypothetical_protein_396452..396682_NEGATIVE 196 69 29 216 171 NC_009009:SSA_1320|5end_hypothetical_protein_1337194..1337424_NEGATIVE 195 43 6 230 182 NC_009009:SSA_0860|5end_N-acetylmuramidase/lysin,_putative_847615..847845_POSITIVE 194 130 84 177 110 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 192 125 85 219 175 NC_009009:SSA_1418|5end_Conserved_uncharacterized_protein_1428927..1429157_NEGATIVE 189 96 57 45 1 NC_009009:SSA_1625|5end_Lactoylglutathione_lyase,_putative_1626963..1627193_NEGATIVE 189 75 31 152 104 NC_009009:SSA_1077|5end_N-acetyl-glucosamine_matabolism,_putative_1094979..1095209_POSITIVE 188 69 28 128 93 NC_009009:SSA_1668|5end_NrdI_protein,_putative_1668091..1668321_NEGATIVE 188 129 82 197 160 NC_009009:SSA_1045|5end_hypothetical_protein_1060841..1061071_POSITIVE 187 128 86 41 1 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 186 87 52 59 23 NC_009009:SSA_0816|5end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797445..797675_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 217 46 6 80 29 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 214 70 40 77 46 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 212 97 56 89 46 NC_009009:SSA_2347|3end_Coenzyme_F390_synthetase,_putative_2348647..2348797_NEGATIVE 209 129 88 72 28 NC_009009:SSA_1319|3end_hypothetical_protein_1336780..1336930_POSITIVE 204 88 50 142 109 NC_009009:SSA_1516|3end_Cell-wall_biogenesis_glycosyltransferase,_putative_1522129..1522279_NEGATIVE 204 28 4 57 31 NC_009009:SSA_0959|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_domain_and_a_winged-helix_DNA-binding_domains),_putative_968596..968746_POSITIVE 202 104 78 76 45 NC_009009:SSA_2385|3end_hypothetical_protein_1752996..1753146_POSITIVE 197 130 84 139 84 NC_009009:SSA_0400|3end_hypothetical_protein_396470..396620_NEGATIVE 194 130 84 77 10 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 194 69 30 55 1 NC_009009:SSA_0730|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_715167..715317_POSITIVE 192 125 85 151 107 NC_009009:SSA_1419|3end_hypothetical_protein_1428995..1429145_NEGATIVE 189 75 31 140 92 NC_009009:SSA_1076|3end_hypothetical_protein_1095047..1095197_POSITIVE 188 69 28 124 89 NC_009009:SSA_1669|3end_hypothetical_protein_1668095..1668245_NEGATIVE 188 129 82 75 38 NC_009009:SSA_1044|3end_Homoserine_kinase,_putative_1060799..1060949_POSITIVE 188 129 85 151 94 NC_009009:SSA_0639|3end_hypothetical_protein_627733..627883_NEGATIVE 187 128 86 48 8 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 186 99 57 71 31 NC_009009:SSA_2005|3end_Chaperone_protein_dnaJ,_putative_2005251..2005401_NEGATIVE 186 102 62 49 5 NC_009009:SSA_1672|3end_hypothetical_protein_1670291..1670441_NEGATIVE 185 104 69 43 10 NC_009009:SSA_1185|3end_DNA_processing_Smf_protein,_putative_1213690..1213840_NEGATIVE 184 127 89 60 21 NC_009009:SSA_1092|3end_Dihydrofolate_reductase,_putative_1110191..1110341_POSITIVE