Origin IGS: tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatgaaaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatatacctccattataacgcgttttcatagttcttttctaatagaatagcataataccttagtattgtcatataaaatcttttcattatttttagcaaacttctatcctcaactacctaagaaaatagttgtatttgtcgcttagttcacgccaca Mask Tandem Repeat Region ================================================ tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatgaaaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta Find is-nt database================================================ Query_seq: SSA_0947:SSA_0948|SSA_0947:SSA_0948:hypothetical protein:hypothetical protein:->->:954937..955094 158 tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatgaaaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0947:SSA_0948|SSA_0947:SSA_0948:hypothetical protein:hypothetical protein:->->:954937..955094 158 tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatgaaaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0947:SSA_0948|SSA_0947:SSA_0948:hypothetical protein:hypothetical protein:->->:954937..955094 158 tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatgaaaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatgaaaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta Predict ORF larger than 30AA ================================================ tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatgaaaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta 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================================================ tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatgaaaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0947:SSA_0948|SSA_0947:SSA_0948:hypothetical protein:hypothetical protein:->->:954937..955094 158 tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatgaaaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta Intra-Species Hit: Count: 2 Min: 1 Max: 158 Len: 158 Subject: NC_009009_SSA_0947_SSA_0948|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[954937,955094]|158 HSP 1 e-value: 9.0E-85 bit: 313.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatgaaaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatgaaaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta Subject: NC_009009_SSA_0948_SSA_0949|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[955689,955846]|158 HSP 1 e-value: 2.0E-49 bit: 196.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatga-aaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta tgtggcgtgaactaagtaacaaatacaaatatttt-ttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUGGCGUGAACUAAGCGACAAAUACAACUAUUUUCUUAGGUAGUUGAGGAUAGAAGUUUGCUAAAAAUAAUGAAAAGAUUUUAUAUGACAAUACUAAGGUAUUAUGCUAUUCUAUUAGAAAAGAACUAUGAAAACGCGUUAUAAUGGAGGUAUAUUA (((((((((................(((((((((....)))))))))..(((((((....((........(((((.....))))).....(((((....)))))..))..)))))))..................))))))))).............. (-27.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUACCUCCAUUAUAACGCGUUUUCAUAGUUCUUUUCUAAUAGAAUAGCAUAAUACCUUAGUAUUGUCAUAUAAAAUCUUUUCAUUAUUUUUAGCAAACUUCUAUCCUCAACUACCUAAGAAAAUAGUUGUAUUUGUCGCUUAGUUCACGCCACA ..............((((((..((((((.(((..........((((((..(.(((((((....))))))))...(((((............)))))......))))))..........))).)))))).))))))..(((.((.........)).))) (-18.05) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 50 4 231 177 NC_009009:SSA_0915|5end_hypothetical_protein_927542..927772_POSITIVE 240 58 16 132 87 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 236 70 25 186 140 NC_009009:SSA_0071|5end_N-acetylmannosamine-6-p_hosphate_2-epimerase_1,_putative_75210..75440_POSITIVE 228 85 41 218 167 NC_009009:SSA_0904|5end_CshA-like_fibrillar_surface_protein_A_893906..894136_POSITIVE 216 53 13 80 42 NC_009009:SSA_2190|5end_33_kDa_chaperonin,_putative_2191166..2191396_POSITIVE 215 74 31 167 113 NC_009009:SSA_0057|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_60762..60992_POSITIVE 209 100 53 229 173 NC_009009:SSA_0594|5end_Transcriptional_regulator,_AraC_family,_putative_585630..585860_POSITIVE 208 63 39 73 48 NC_009009:SSA_2078|5end_hypothetical_protein_2083837..2084067_NEGATIVE 208 59 11 97 39 NC_009009:SSA_1607|5end_Formamidopyrimidine-DNA_glycosylase,_putative_1613255..1613485_NEGATIVE 206 69 25 56 12 NC_009009:SSA_0329|5end_Glycerol_uptake_facilitator/aquaporin_protein,_putative_322830..323060_POSITIVE 204 45 4 88 48 NC_009009:SSA_1262|5end_tRNA_modification_GTPase,_possibly_iron-binding,_putative_1287782..1288012_POSITIVE 202 50 15 71 18 NC_009009:SSA_0606|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_594532..594762_NEGATIVE 201 63 25 215 183 NC_009009:SSA_1217|5end_Conserved_uncharacterized_protein_1238964..1239194_POSITIVE 200 140 95 71 19 NC_009009:SSA_1696|5end_Tagatose_1,6-diphosphate_aldolase_2,_putative_1689187..1689417_NEGATIVE 196 62 39 26 3 NC_009009:SSA_2144|5end_Glutamyl-tRNA_synthetase,_putative_2145772..2146002_NEGATIVE 195 48 1 165 116 NC_009009:SSA_0836|5end_SecA-like_protein,_putative_821508..821738_POSITIVE 193 26 1 181 147 NC_009009:SSA_2033|5end_30S_ribosomal_protein_S9,_putative_2038779..2039009_NEGATIVE 190 59 15 145 98 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 188 63 38 127 103 NC_009009:SSA_2210|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_2210475..2210705_POSITIVE 187 150 101 229 187 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 51 12 47 1 NC_009009:SSA_0914|3end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_927437..927587_POSITIVE 243 60 11 82 41 NC_009009:SSA_1810|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1794707..1794857_NEGATIVE 240 58 16 126 81 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 209 100 53 70 14 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 208 59 11 69 11 NC_009009:SSA_1608|3end_hypothetical_protein_1613283..1613433_NEGATIVE 200 140 95 67 15 NC_009009:SSA_1697|3end_Tagatose-6-phosphate_kinase,_putative_1689191..1689341_NEGATIVE 197 63 24 149 118 NC_009009:SSA_0718|3end_Conserved_uncharacterized_protein_704935..705085_POSITIVE 196 63 30 142 100 NC_009009:SSA_0056|3end_Phosphotransferase_system_sugar-specific_EIID_component,_putative_60830..60980_POSITIVE 190 59 15 87 40 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 183 59 40 91 72 NC_009009:SSA_1552|3end_hypothetical_protein_1555130..1555280_POSITIVE 183 49 1 69 26 NC_009009:SSA_0868|3end_hypothetical_protein_860675..860825_NEGATIVE 182 126 87 150 120 NC_009009:SSA_1161|3end_hypothetical_protein_1188443..1188593_POSITIVE 182 110 61 148 98 NC_009009:SSA_0872|3end_Zn-dependent_hydrolases,_including_glyoxylases,_putative_864667..864817_NEGATIVE 181 74 31 148 99 NC_009009:SSA_0290|3end_hypothetical_protein_284084..284234_NEGATIVE 179 57 29 31 5 NC_009009:SSA_0292|3end_Transcriptional_regulator,_AraC_family_(arabinose_operon_control),_putative_287262..287412_POSITIVE 178 47 1 145 99 NC_009009:SSA_1396|3end_hypothetical_protein_1409790..1409940_NEGATIVE 178 60 15 82 41 NC_009009:SSA_0201|3end_ABC_multidrug_transporter_(3-component_subtilin_immunity_exporter),_putative_200612..200762_POSITIVE 177 63 29 139 91 NC_009009:SSA_1262|3end_tRNA_modification_GTPase,_possibly_iron-binding,_putative_1289235..1289385_POSITIVE 177 49 1 74 22 NC_009009:SSA_0966|3end_Uridine_kinase,_putative_975790..975940_POSITIVE 176 78 36 58 20 NC_009009:SSA_0643|3end_hypothetical_protein_630072..630222_NEGATIVE