Origin IGS: aggaactcctcctttatctgatggatagcgcttacctatattatactcctaatcatgagaattgtcagaaaataacactttcgcacaaaaaaacggccgcagccgtttcctctatttatcact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtgataaatagaggaaacggctgcggccgtttttttgtgcgaaagtgttattttctgacaattctcatgattaggagtataatataggtaagcgctatccatcagataaaggaggagttcct Mask Tandem Repeat Region ================================================ aggaactcctcctttatctgatggatagcgcttacctatattatactcctaatcatgagaattgtcagaaaataacactttcgcacaaaaaaacggccgcagccgtttcctctatttatcact Find is-nt database================================================ Query_seq: SSA_1269:SSA_1270|SSA_1269:SSA_1270:hypothetical protein:Flavodoxin:<-<-:1293443..1293565 123 aggaactcctcctttatctgatggatagcgcttacctatattatactcctaatcatgagaattgtcagaaaataacactttcgcacaaaaaaacggccgcagccgtttcctctatttatcact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1269:SSA_1270|SSA_1269:SSA_1270:hypothetical protein:Flavodoxin:<-<-:1293443..1293565 123 aggaactcctcctttatctgatggatagcgcttacctatattatactcctaatcatgagaattgtcagaaaataacactttcgcacaaaaaaacggccgcagccgtttcctctatttatcact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1269:SSA_1270|SSA_1269:SSA_1270:hypothetical protein:Flavodoxin:<-<-:1293443..1293565 123 aggaactcctcctttatctgatggatagcgcttacctatattatactcctaatcatgagaattgtcagaaaataacactttcgcacaaaaaaacggccgcagccgtttcctctatttatcact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggaactcctcctttatctgatggatagcgcttacctatattatactcctaatcatgagaattgtcagaaaataacactttcgcacaaaaaaacggccgcagccgtttcctctatttatcact Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 18 End: 122 ................. M M D S A Y L Y Y T P N H E N C Q K I T L S H K K T A A A V S S I Y H . aggaactcctcctttatctgatggatagcgcttacctatattatactcctaatcatgagaattgtcagaaaataacactttcgcacaaaaaaacggccgcagccgtttcctctatttatcact 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: 87 Start: 40 End: 69 .......................................TCTGACAATTCTCATGATTAGGAGTATAAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggaactcctcctttatctgatggatagcgcttacctatattatactcctaatcatgagaattgtcagaaaataacactttcgcacaaaaaaacggccgcagccgtttcctctatttatcact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 72 HP_score: -7.2 Tail_Score: -3.98915 Start: 94 End: 105 Full_Region: TTTCGCACAAAAAAA CGGC CGCA GCCG TTTCCTCTATTTATC .............................................................................................CGGCCGCAGCCG.................. Find igs database================================================ Query_seq: SSA_1269:SSA_1270|SSA_1269:SSA_1270:hypothetical protein:Flavodoxin:<-<-:1293443..1293565 123 aggaactcctcctttatctgatggatagcgcttacctatattatactcctaatcatgagaattgtcagaaaataacactttcgcacaaaaaaacggccgcagccgtttcctctatttatcact Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: NC_009009_SSA_1269_SSA_1270|hypothetical protein:Flavodoxin|NEGATIVE:NEGATIVE|[1293443, 1293565]|123 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 aggaactcctcctttatctgatggatagcgcttacctatattatactcctaatcatgagaattgtcagaaaataacactttcgcacnnnnnnncggccgcagccgtttcctctatttatcact aggaactcctcctttatctgatggatagcgcttacctatattatactcctaatcatgagaattgtcagaaaataacactttcgcacaaaaaaacggccgcagccgtttcctctatttatcact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAACUCCUCCUUUAUCUGAUGGAUAGCGCUUACCUAUAUUAUACUCCUAAUCAUGAGAAUUGUCAGAAAAUAACACUUUCGCACAAAAAAACGGCCGCAGCCGUUUCCUCUAUUUAUCACU ((((.....)))).....((((((((((.(...............(((........)))..((((..((((.......))))..))))..(((((((....))))))).).)))))))))).. (-23.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGAUAAAUAGAGGAAACGGCUGCGGCCGUUUUUUUGUGCGAAAGUGUUAUUUUCUGACAAUUCUCAUGAUUAGGAGUAUAAUAUAGGUAAGCGCUAUCCAUCAGAUAAAGGAGGAGUUCCU ..((((.....(((((((((((....)))))))))))((((....((((((((((((((((.......)).))))))).)))))))......)))).....)))).....(((((...))))) (-29.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 903 110 61 201 152 NC_009009:SSA_1269|5end_hypothetical_protein_1293352..1293582_NEGATIVE 358 117 81 184 143 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 312 99 51 222 176 NC_009009:SSA_1612|5end_Diacylglycerol_kinase,_putative_1616497..1616727_NEGATIVE 309 109 61 138 77 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 296 33 1 128 93 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 274 38 1 134 93 NC_009009:SSA_1764|5end_hypothetical_protein_1750868..1751098_POSITIVE 261 48 2 144 92 NC_009009:SSA_0701|5end_Cation_transporter_CorA_family,_putative_684368..684598_POSITIVE 259 50 7 109 74 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 259 110 79 35 4 NC_009009:SSA_0086|5end_V-type_sodium_ATPase,_subunit_K,_putative_87839..88069_POSITIVE 256 113 78 228 197 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 251 32 1 145 92 NC_009009:SSA_0042|5end_Amino_acid_recemase,_putative_47893..48123_POSITIVE 250 110 62 68 27 NC_009009:SSA_2198|5end_hypothetical_protein_2198585..2198815_NEGATIVE 247 112 77 62 20 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 246 105 78 192 168 NC_009009:SSA_1281|5end_Uracil-DNA_glycosylase,_putative_1302192..1302422_NEGATIVE 246 104 66 43 1 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 246 46 6 129 97 NC_009009:SSA_0095|5end_Threonine_synthase,_putative_96555..96785_POSITIVE 245 112 78 52 4 NC_009009:SSA_1493|5end_hypothetical_protein_1499480..1499710_NEGATIVE 244 50 1 101 42 NC_009009:SSA_1236|5end_Mutator_protein,_putative_1261704..1261934_NEGATIVE 244 109 65 206 153 NC_009009:SSA_0450|5end_Elongation_factor_P,_putative_450587..450817_POSITIVE 243 113 78 98 46 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 106 62 79 34 NC_009009:SSA_0259|3end_Thiol_peroxidase,_putative_253013..253163_NEGATIVE 296 33 1 128 93 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 274 38 1 137 96 NC_009009:SSA_1763|3end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750951..1751101_POSITIVE 259 50 7 99 64 NC_009009:SSA_0238|3end_hypothetical_protein_233031..233181_POSITIVE 251 117 88 96 61 NC_009009:SSA_0774|3end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase,_putative_756075..756225_POSITIVE 251 32 1 141 88 NC_009009:SSA_0041|3end_hypothetical_protein_47969..48119_POSITIVE 246 105 78 138 114 NC_009009:SSA_1282|3end_Dipeptidase_V,_putative_1302246..1302396_NEGATIVE 244 50 1 92 33 NC_009009:SSA_1237|3end_Uracil-DNA_glycosylase,_putative_1261713..1261863_NEGATIVE 244 109 65 144 91 NC_009009:SSA_0449|3end_Aminopeptidase_P;_XAA-pro_aminopeptidase,_putative_450605..450755_POSITIVE 243 113 78 105 53 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 242 103 67 72 37 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 242 113 96 142 123 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 239 50 6 141 102 NC_009009:SSA_0155|3end_hypothetical_protein_151406..151556_POSITIVE 238 110 62 56 3 NC_009009:SSA_0364|3end_Serine/threonine:Na+_symporter,_putative_355311..355461_NEGATIVE 236 110 94 60 41 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 235 111 92 30 11 NC_009009:SSA_1561|3end_Ribonuclease_III,_putative_1565185..1565335_NEGATIVE 234 115 78 146 98 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE 234 37 4 151 112 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 231 119 77 94 38 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 230 112 96 78 56 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE