Origin IGS: taaatcgataatttcacttcaaatcaaaaagttccgattttccttgagaatcggaactttagatttgatgacaggtgagcaaaggtttaggtgtaagtcaaacgaagctgttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaacagcttcgtttgacttacacctaaacctttgctcacctgtcatcaaatctaaagttccgattctcaaggaaaatcggaactttttgatttgaagtgaaattatcgattta Mask Tandem Repeat Region ================================================ taaatcgataatttcacttcaaatcaaaaagttccgattttccttgagaatcggaactttagatttgatgacaggtgagcaaaggtttaggtgtaagtcaaacgaagctgttt Find is-nt database================================================ Query_seq: SSA_0253:SSA_0254|SSA_0253:SSA_0254:CAAX amino terminal protease family protein, putative:hypothetical protein:-><-:247044..247156 113 taaatcgataatttcacttcaaatcaaaaagttccgattttccttgagaatcggaactttagatttgatgacaggtgagcaaaggtttaggtgtaagtcaaacgaagctgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0253:SSA_0254|SSA_0253:SSA_0254:CAAX amino terminal protease family protein, putative:hypothetical protein:-><-:247044..247156 113 taaatcgataatttcacttcaaatcaaaaagttccgattttccttgagaatcggaactttagatttgatgacaggtgagcaaaggtttaggtgtaagtcaaacgaagctgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0253:SSA_0254|SSA_0253:SSA_0254:CAAX amino terminal protease family protein, putative:hypothetical protein:-><-:247044..247156 113 taaatcgataatttcacttcaaatcaaaaagttccgattttccttgagaatcggaactttagatttgatgacaggtgagcaaaggtttaggtgtaagtcaaacgaagctgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatcgataatttcacttcaaatcaaaaagttccgattttccttgagaatcggaactttagatttgatgacaggtgagcaaaggtttaggtgtaagtcaaacgaagctgttt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 8 End: 112 ....... M I S L Q I K K F R F S L R I G T L D L M T G E Q R F R C K S N E A V . taaatcgataatttcacttcaaatcaaaaagttccgattttccttgagaatcggaactttagatttgatgacaggtgagcaaaggtttaggtgtaagtcaaacgaagctgttt 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================================================ taaatcgataatttcacttcaaatcaaaaagttccgattttccttgagaatcggaactttagatttgatgacaggtgagcaaaggtttaggtgtaagtcaaacgaagctgttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -11.0 Tail_Score: -3.73224 Start: 24 End: 63 Full_Region: TAATTTCACTTCAAA TCAAAAAGTTCCGATTTTC CTT GAGAATCGGAACTTTAGA TTTGATGACAGGTGA .......................TCAAAAAGTTCCGATTTTCCTTGAGAATCGGAACTTTAGA.................................................. TransTerm Strand: - Conf: 100 HP_score: -12.4 Tail_Score: -4.99134 Start: 31 End: 57 Full_Region: gtcatcaaatctaaa gttccgattctc aag gaaaatcggaac tttttgatttgaagt ..............................gttccgattctcaaggaaaatcggaac........................................................ Find igs database================================================ Query_seq: SSA_0253:SSA_0254|SSA_0253:SSA_0254:CAAX amino terminal protease family protein, putative:hypothetical protein:-><-:247044..247156 113 taaatcgataatttcacttcaaatcaaaaagttccgattttccttgagaatcggaactttagatttgatgacaggtgagcaaaggtttaggtgtaagtcaaacgaagctgttt Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: NC_009009_SSA_0253_SSA_0254|CAAX amino terminal protease family protein, putative:hypothetical protein|POSITIVE:NEGATIVE|[247044,247156]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 taaatcgataatttcacttcaaatcaaaaagttccgattttccttgagaatcggaactttagatttgatgacaggtgagcaaaggtttaggtgtaagtcaaacgaagctgttt taaatcgataatttcacttcaaatcaaaaagttccgattttccttgagaatcggaactttagatttgatgacaggtgagcaaaggtttaggtgtaagtcaaacgaagctgttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCGAUAAUUUCACUUCAAAUCAAAAAGUUCCGAUUUUCCUUGAGAAUCGGAACUUUAGAUUUGAUGACAGGUGAGCAAAGGUUUAGGUGUAAGUCAAACGAAGCUGUUU ......((((.((((...(((((((..(((((((((((((((...))))))))))))))).)))))))..(((..(((((....)))))..))).........)))).)))). (-32.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACAGCUUCGUUUGACUUACACCUAAACCUUUGCUCACCUGUCAUCAAAUCUAAAGUUCCGAUUCUCAAGGAAAAUCGGAACUUUUUGAUUUGAAGUGAAAUUAUCGAUUUA ....(((...(((((.........)))))....)))......((((((((((.((((((((((((.((...)).))))))))))))..)))))))..)))............. (-26.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 79 34 69 33 NC_009009:SSA_0436|5end_Imidazolonepropionase,_putative_438869..439099_POSITIVE 265 96 51 219 179 NC_009009:SSA_1953|5end_NifU_family_protein,_putative_1950079..1950309_NEGATIVE 259 108 64 231 190 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 246 110 69 60 30 NC_009009:SSA_0898|5end_hypothetical_protein_889863..890093_NEGATIVE 244 79 34 69 30 NC_009009:SSA_0905|5end_CshA-like_fibrillar_surface_protein_B_903080..903310_POSITIVE 244 49 1 169 118 NC_009009:SSA_0270|5end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_262873..263103_POSITIVE 243 87 41 135 78 NC_009009:SSA_0295|5end_Transcriptional_regulator,_LysR_family,_putative_288901..289131_NEGATIVE 242 110 63 68 26 NC_009009:SSA_0214|5end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210215..210445_POSITIVE 236 80 31 97 34 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 235 80 34 68 11 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 234 77 35 181 144 NC_009009:SSA_2302|5end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2304044..2304274_NEGATIVE 234 80 34 66 31 NC_009009:SSA_1386|5end_NADPH-dependent_FMN_reductase,_putative_1402800..1403030_POSITIVE 233 100 51 227 183 NC_009009:SSA_2188|5end_Conserved_uncharacterized_protein_2188896..2189126_POSITIVE 232 91 58 122 91 NC_009009:SSA_1926|5end_hypothetical_protein_1914829..1915059_POSITIVE 232 109 72 47 10 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 232 46 14 229 195 NC_009009:SSA_1383|5end_Aspartate_aminotransferase,_putative_1401718..1401948_NEGATIVE 231 100 51 189 150 NC_009009:SSA_0510|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_508523..508753_POSITIVE 230 77 36 206 162 NC_009009:SSA_1424|5end_Hydrolase,_putative_1434479..1434709_NEGATIVE 229 90 41 58 18 NC_009009:SSA_1779|5end_Segregation_and_condensation_protein_A,_putative_1766414..1766644_NEGATIVE 229 110 63 54 2 NC_009009:SSA_0588|5end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_579800..580030_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 456 68 23 72 22 NC_009009:SSA_0253|3end_CAAX_amino_terminal_protease_family_protein,_putative_246983..247133_POSITIVE 258 108 68 45 1 NC_009009:SSA_0608|3end_Macrolide-efflux_protein,_putative_596901..597051_NEGATIVE 252 100 57 59 4 NC_009009:SSA_2077|3end_hypothetical_protein_2081352..2081502_NEGATIVE 251 88 45 137 94 NC_009009:SSA_2155|3end_hypothetical_protein_2155407..2155557_NEGATIVE 246 75 35 151 96 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 243 94 51 110 57 NC_009009:SSA_2348|3end_Metal_dependent_hydrolase,_putative_2349875..2350025_NEGATIVE 243 80 31 64 13 NC_009009:SSA_1417|3end_SAM-dependent_methyltransferase,_putative_1427304..1427454_NEGATIVE 236 75 32 115 74 NC_009009:SSA_1625|3end_Lactoylglutathione_lyase,_putative_1626577..1626727_NEGATIVE 236 80 31 86 23 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 234 77 35 112 75 NC_009009:SSA_2303|3end_hypothetical_protein_2304113..2304263_NEGATIVE 232 91 58 78 47 NC_009009:SSA_1925|3end_Seryl-tRNA_synthetase,_putative_1914865..1915015_POSITIVE 231 100 51 124 85 NC_009009:SSA_0509|3end_Propanediol_utilization_protein,_putative_508538..508688_POSITIVE 230 38 1 150 112 NC_009009:SSA_0269|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262947..263097_POSITIVE 229 90 41 56 16 NC_009009:SSA_1780|3end_Tyrosine_recombinase_xerD,_putative_1766416..1766566_NEGATIVE 228 100 53 125 74 NC_009009:SSA_0709|3end_hypothetical_protein_695632..695782_NEGATIVE 227 110 81 78 55 NC_009009:SSA_1747|3end_hypothetical_protein_1732938..1733088_NEGATIVE 227 110 61 59 18 NC_009009:SSA_0803|3end_hypothetical_protein_785980..786130_POSITIVE 223 54 17 77 48 NC_009009:SSA_0177|3end_DNA-directed_RNA_polymerase_I,_beta_chain_(160_kDa_subunit),_putative_182132..182282_POSITIVE 222 60 17 72 31 NC_009009:SSA_1292|3end_hypothetical_protein_1311099..1311249_NEGATIVE 222 90 44 66 7 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE