Origin IGS: ttccggtgcaaccaaggagccctcatctacgccaatagatgagggctccggctttattctgggagaatttctataaaaaaactctcacctacgccaatagatgagagccctcgattgtacatgcatacaacctatcacggaattatattgtaacttattttttataccttgtcaagtgttatataaaaatagtatgtgtcatagattttgagaagataaaaaatctaaactcactaacaactatttagaaaattatatcctgccagaatggttcattaaaaaactctcatctacgccaatagatgagagtcctcgattgtacatgcatacaacctatcctaggtatactattttagccccttttttatactttgtcaagcttcacctagaatagaataactacatacgtcaaaagccccacctaatcacaataggtgggactttgaataatatgcctgttgtagacttttttatttctacttaaatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgatttaagtagaaataaaaaagtctacaacaggcatattattcaaagtcccacctattgtgattaggtggggcttttgacgtatgtagttattctattctaggtgaagcttgacaaagtataaaaaaggggctaaaatagtatacctaggataggttgtatgcatgtacaatcgaggactctcatctattggcgtagatgagagttttttaatgaaccattctggcaggatataattttctaaatagttgttagtgagtttagattttttatcttctcaaaatctatgacacatactatttttatataacacttgacaaggtataaaaaataagttacaatataattccgtgataggttgtatgcatgtacaatcgagggctctcatctattggcgtaggtgagagtttttttatagaaattctcccagaataaagccggagccctcatctattggcgtagatgagggctccttggttgcaccggaa Mask Tandem Repeat Region ================================================ ttccggtgcaaccaaggagccctcatctacgccaatagatgagggctccggctttattctgggagaatttctataaaaaaactctcacctacgccaatagatgagagccctcgattgtacatgcatacaacctatcacggaattatattgtaacttattttttataccttgtcaagtgttatataaaaatagtatgtgtcatagattttgagaagataaaaaatctaaactcactaacaactatttagaaaattatatcctgccagaatggttcattaaaaaactctcatctacgccaatagatgagagtcctcgattgtacatgcatacaacctatcctaggtatactattttagccccttttttatactttgtcaagcttcacctagaatagaataactacatacgtcaaaagccccacctaatcacaataggtgggactttgaataatatgcctgttgtagacttttttatttctacttaaatca Find is-nt database================================================ Query_seq: SSA_2206:SSA_2208|SSA_2206:SSA_2208:hypothetical protein:Preprotein translocase secE component, putative:-><-:2207336..2207823 488 ttccggtgcaaccaaggagccctcatctacgccaatagatgagggctccggctttattctgggagaatttctataaaaaaactctcacctacgccaatagatgagagccctcgattgtacatgcatacaacctatcacggaattatattgtaacttattttttataccttgtcaagtgttatataaaaatagtatgtgtcatagattttgagaagataaaaaatctaaactcactaacaactatttagaaaattatatcctgccagaatggttcattaaaaaactctcatctacgccaatagatgagagtcctcgattgtacatgcatacaacctatcctaggtatactattttagccccttttttatactttgtcaagcttcacctagaatagaataactacatacgtcaaaagccccacctaatcacaataggtgggactttgaataatatgcctgttgtagacttttttatttctacttaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2206:SSA_2208|SSA_2206:SSA_2208:hypothetical protein:Preprotein translocase secE component, putative:-><-:2207336..2207823 488 ttccggtgcaaccaaggagccctcatctacgccaatagatgagggctccggctttattctgggagaatttctataaaaaaactctcacctacgccaatagatgagagccctcgattgtacatgcatacaacctatcacggaattatattgtaacttattttttataccttgtcaagtgttatataaaaatagtatgtgtcatagattttgagaagataaaaaatctaaactcactaacaactatttagaaaattatatcctgccagaatggttcattaaaaaactctcatctacgccaatagatgagagtcctcgattgtacatgcatacaacctatcctaggtatactattttagccccttttttatactttgtcaagcttcacctagaatagaataactacatacgtcaaaagccccacctaatcacaataggtgggactttgaataatatgcctgttgtagacttttttatttctacttaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2206:SSA_2208|SSA_2206:SSA_2208:hypothetical protein:Preprotein translocase secE component, putative:-><-:2207336..2207823 488 ttccggtgcaaccaaggagccctcatctacgccaatagatgagggctccggctttattctgggagaatttctataaaaaaactctcacctacgccaatagatgagagccctcgattgtacatgcatacaacctatcacggaattatattgtaacttattttttataccttgtcaagtgttatataaaaatagtatgtgtcatagattttgagaagataaaaaatctaaactcactaacaactatttagaaaattatatcctgccagaatggttcattaaaaaactctcatctacgccaatagatgagagtcctcgattgtacatgcatacaacctatcctaggtatactattttagccccttttttatactttgtcaagcttcacctagaatagaataactacatacgtcaaaagccccacctaatcacaataggtgggactttgaataatatgcctgttgtagacttttttatttctacttaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttccggtgcaaccaaggagccctcatctacgccaatagatgagggctccggctttattctgggagaatttctataaaaaaactctcacctacgccaatagatgagagccctcgattgtacatgcatacaacctatcacggaattatattgtaacttattttttataccttgtcaagtgttatataaaaatagtatgtgtcatagattttgagaagataaaaaatctaaactcactaacaactatttagaaaattatatcctgccagaatggttcattaaaaaactctcatctacgccaatagatgagagtcctcgattgtacatgcatacaacctatcctaggtatactattttagccccttttttatactttgtcaagcttcacctagaatagaataactacatacgtcaaaagccccacctaatcacaataggtgggactttgaataatatgcctgttgtagacttttttatttctacttaaatca Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 101 End: 208 .................................................................................................... M R A L D C T C I Q P I T E L Y C N L F F I P C Q V L Y K N S M C H R F ........................................................................................................................................................................................................................................................................................ Protein_Len: 44 Strand: + Start: 114 End: 245 ................................................................................................................. M V H A Y N L S R N Y I V T Y F L Y L V K C Y I K I V C V I D F E K I K N L N S L T T I ................................................................................................................................................................................................................................................... Protein_Len: 45 Strand: + Start: 257 End: 391 ................................................................................................................................................................................................................................................................ M L P E W F I K K L S S T P I D E S P R L Y M H T T Y P R Y T I L A P F L Y F V K L H L E ................................................................................................. ttccggtgcaaccaaggagccctcatctacgccaatagatgagggctccggctttattctgggagaatttctataaaaaaactctcacctacgccaatagatgagagccctcgattgtacatgcatacaacctatcacggaattatattgtaacttattttttataccttgtcaagtgttatataaaaatagtatgtgtcatagattttgagaagataaaaaatctaaactcactaacaactatttagaaaattatatcctgccagaatggttcattaaaaaactctcatctacgccaatagatgagagtcctcgattgtacatgcatacaacctatcctaggtatactattttagccccttttttatactttgtcaagcttcacctagaatagaataactacatacgtcaaaagccccacctaatcacaataggtgggactttgaataatatgcctgttgtagacttttttatttctacttaaatca 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: 89 Start: 350 End: 379 .............................................................................................................................................................................................................................................................................................................................................................CTTGACAAAGTATAAAAAAGGGGCTAAAAT............................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 88 Start: 147 End: 176 ..................................................................................................................................................CTTGACAAGGTATAAAAAATAAGTTACAAT........................................................................................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 363 End: 392 ..........................................................................................................................................................................................................................................................................................................................................................................TTTTATACTTTGTCAAGCTTCACCTAGAAT................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 252 End: 281 ...........................................................................................................................................................................................................................................................TTTTAATGAACCATTCTGGCAGGATATAAT............................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttccggtgcaaccaaggagccctcatctacgccaatagatgagggctccggctttattctgggagaatttctataaaaaaactctcacctacgccaatagatgagagccctcgattgtacatgcatacaacctatcacggaattatattgtaacttattttttataccttgtcaagtgttatataaaaatagtatgtgtcatagattttgagaagataaaaaatctaaactcactaacaactatttagaaaattatatcctgccagaatggttcattaaaaaactctcatctacgccaatagatgagagtcctcgattgtacatgcatacaacctatcctaggtatactattttagccccttttttatactttgtcaagcttcacctagaatagaataactacatacgtcaaaagccccacctaatcacaataggtgggactttgaataatatgcctgttgtagacttttttatttctacttaaatca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -18.2 Tail_Score: -2.60075 Start: 17 End: 48 Full_Region: cccagaataaagccg gagccctcatctat tggc gtagatgagggctc cttggttgcaccgga ................gagccctcatctattggcgtagatgagggctc........................................................................................................................................................................................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -15.0 Tail_Score: -2.84098 Start: 19 End: 46 Full_Region: cagaataaagccgga gccctcatctat tggc gtagatgagggc tccttggttgcaccg ..................gccctcatctattggcgtagatgagggc.......................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -9.1 Tail_Score: -5.61596 Start: 82 End: 107 Full_Region: atgtacaatcgaggg ctctcatctat tggc gtaggtgagag tttttttatagaaat .................................................................................ctctcatctattggcgtaggtgagag............................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 47 HP_score: -4.5 Tail_Score: -2.6063 Start: 281 End: 312 Full_Region: GAATGGTTCATTAAA AAACTCTCATCTA CGCCAA TAGATGAGAGTCC TCGATTGTACATGCA ........................................................................................................................................................................................................................................................................................AAACTCTCATCTACGCCAATAGATGAGAGTCC................................................................................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -11.3 Tail_Score: -5.14563 Start: 284 End: 309 Full_Region: atgtacaatcgagga ctctcatctat tggc gtagatgagag ttttttaatgaacca ...........................................................................................................................................................................................................................................................................................ctctcatctattggcgtagatgagag................................................................................................................................................................................... TransTerm Strand: - Conf: 91 HP_score: -11.6 Tail_Score: -4.18401 Start: 415 End: 441 Full_Region: ggcatattattcaaa gtcccacctatt gtg attaggtggggc ttttgacgtatgtag ..............................................................................................................................................................................................................................................................................................................................................................................................................................gtcccacctattgtgattaggtggggc............................................... Find igs database================================================ Query_seq: SSA_2206:SSA_2208|SSA_2206:SSA_2208:hypothetical protein:Preprotein translocase secE component, putative:-><-:2207336..2207823 488 ttccggtgcaaccaaggagccctcatctacgccaatagatgagggctccggctttattctgggagaatttctataaaaaaactctcacctacgccaatagatgagagccctcgattgtacatgcatacaacctatcacggaattatattgtaacttattttttataccttgtcaagtgttatataaaaatagtatgtgtcatagattttgagaagataaaaaatctaaactcactaacaactatttagaaaattatatcctgccagaatggttcattaaaaaactctcatctacgccaatagatgagagtcctcgattgtacatgcatacaacctatcctaggtatactattttagccccttttttatactttgtcaagcttcacctagaatagaataactacatacgtcaaaagccccacctaatcacaataggtgggactttgaataatatgcctgttgtagacttttttatttctacttaaatca Intra-Species Hit: Count: 1 Min: 1 Max: 488 Len: 488 Subject: NC_009009_SSA_2206_SSA_2208|hypothetical protein:Preprotein translocase secE component, putative|POSITIVE:NEGATIVE|[2207336,2207823]|488 HSP 1 e-value: 0.0 bit: 926.0 Len: 488 Query Start:1 Query End:488 Subject Strand: POSITIVE Subject Start: 1 Subject End: 488 ttccggtgcaaccaaggagccctcatctacgccaatagatgagggctccggctttattctgggagaatttctatnnnnnnnctctcacctacgccaatagatgagagccctcgattgtacatgcatacaacctatcacggaattatattgtaacttattttttataccttgtcaagtgttatataaaaatagtatgtgtcatagattttgagaagataaaaaatctaaactcactaacaactatttagaaaattatatcctgccagaatggttcattaaaaaactctcatctacgccaatagatgagagtcctcgattgtacatgcatacaacctatcctaggtatactattttagccccttttttatactttgtcaagcttcacctagaatagaataactacatacgtcaaaagccccacctaatcacaataggtgggactttgaataatatgcctgttgtagacttttttatttctacttaaatca ttccggtgcaaccaaggagccctcatctacgccaatagatgagggctccggctttattctgggagaatttctataaaaaaactctcacctacgccaatagatgagagccctcgattgtacatgcatacaacctatcacggaattatattgtaacttattttttataccttgtcaagtgttatataaaaatagtatgtgtcatagattttgagaagataaaaaatctaaactcactaacaactatttagaaaattatatcctgccagaatggttcattaaaaaactctcatctacgccaatagatgagagtcctcgattgtacatgcatacaacctatcctaggtatactattttagccccttttttatactttgtcaagcttcacctagaatagaataactacatacgtcaaaagccccacctaatcacaataggtgggactttgaataatatgcctgttgtagacttttttatttctacttaaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCGGUGCAACCAAGGAGCCCUCAUCUACGCCAAUAGAUGAGGGCUCCGGCUUUAUUCUGGGAGAAUUUCUAUAAAAAAACUCUCACCUACGCCAAUAGAUGAGAGCCCUCGAUUGUACAUGCAUACAACCUAUCACGGAAUUAUAUUGUAACUUAUUUUUUAUACCUUGUCAAGUGUUAUAUAAAAAUAGUAUGUGUCAUAGAUUUUGAGAAGAUAAAAAAUCUAAACUCACUAACAACUAUUUAGAAAAUUAUAUCCUGCCAGAAUGGUUCAUUAAAAAACUCUCAUCUACGCCAAUAGAUGAGAGUCCUCGAUUGUACAUGCAUACAACCUAUCCUAGGUAUACUAUUUUAGCCCCUUUUUUAUACUUUGUCAAGCUUCACCUAGAAUAGAAUAACUACAUACGUCAAAAGCCCCACCUAAUCACAAUAGGUGGGACUUUGAAUAAUAUGCCUGUUGUAGACUUUUUUAUUUCUACUUAAAUCA ...(((.(((.....((((((((((((((......))))))))))))))...(((((((((((.(((....(((((((((.((((((.(((......))).))))))..........((((...(((...((......))...)))..)))).....))))))))).((((.(((((((.......(((((((..(((...((((((((..........))))))))....))).....)))))))...............((.((((((((..........(((((((((((......))))))))))).....................(((((...)))))..)))))))).)).........)))).))).)))).))).))))))))))).............(((((.(.((((((((.......)))))))).))))))......))))))..(((((..(....)..)))))........ (-126.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUAAGUAGAAAUAAAAAAGUCUACAACAGGCAUAUUAUUCAAAGUCCCACCUAUUGUGAUUAGGUGGGGCUUUUGACGUAUGUAGUUAUUCUAUUCUAGGUGAAGCUUGACAAAGUAUAAAAAAGGGGCUAAAAUAGUAUACCUAGGAUAGGUUGUAUGCAUGUACAAUCGAGGACUCUCAUCUAUUGGCGUAGAUGAGAGUUUUUUAAUGAACCAUUCUGGCAGGAUAUAAUUUUCUAAAUAGUUGUUAGUGAGUUUAGAUUUUUUAUCUUCUCAAAAUCUAUGACACAUACUAUUUUUAUAUAACACUUGACAAGGUAUAAAAAAUAAGUUACAAUAUAAUUCCGUGAUAGGUUGUAUGCAUGUACAAUCGAGGGCUCUCAUCUAUUGGCGUAGGUGAGAGUUUUUUUAUAGAAAUUCUCCCAGAAUAAAGCCGGAGCCCUCAUCUAUUGGCGUAGAUGAGGGCUCCUUGGUUGCACCGGAA ......................((.((((((..((((((...(((((((((((((((.......)))))))))).))))).)))))).......((((((((((((..((((....))))...........((((...)))).)))))))))))))))))).)).....((.(.((((((((((((((((....)))))))))))))))).).))..((.((((((.(((((..........((((((((((((.((((...((((.....)))).)))).......)))))...)))))))....................(((((((((...(((((...........))))).((((((((....))))))))....((((((((((((....)))))))))))))))))))))...))))).))))))...(((((((((((((((((((....)))))))))))))))..)))).....)).. (-157.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1088 50 1 165 116 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 351 55 12 45 1 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 346 55 11 75 19 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 341 45 1 76 36 NC_009009:SSA_0833|5end_Accessory_secretory_protein_Asp1,_putative_817940..818170_POSITIVE 340 48 1 198 153 NC_009009:SSA_1725|5end_Branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1711703..1711933_NEGATIVE 336 60 19 223 190 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 335 140 91 214 170 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 332 49 5 145 94 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 325 44 4 180 132 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 322 52 12 61 16 NC_009009:SSA_0498|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_systems,_permease_components,_putative_497910..498140_POSITIVE 316 50 3 222 178 NC_009009:SSA_1612|5end_Diacylglycerol_kinase,_putative_1616497..1616727_NEGATIVE 315 54 11 200 146 NC_009009:SSA_1381|5end_hypothetical_protein_1399565..1399795_NEGATIVE 311 52 17 41 2 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 309 46 3 161 125 NC_009009:SSA_0789|5end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772451..772681_POSITIVE 309 70 21 80 34 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 307 59 15 64 2 NC_009009:SSA_0885|5end_hypothetical_protein_879514..879744_NEGATIVE 306 71 37 184 150 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 303 340 295 103 46 NC_009009:SSA_0166|5end_hypothetical_protein_164641..164871_POSITIVE 302 56 15 87 45 NC_009009:SSA_0663|5end_Acetyltransferase,_putative_648352..648582_POSITIVE 301 70 22 60 20 NC_009009:SSA_0996|5end_cGMP-specific_phosphodiesterase,_putative_996282..996512_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 570 49 1 75 27 NC_009009:SSA_2206|3end_hypothetical_protein_2207275..2207425_POSITIVE 375 141 101 131 93 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 359 49 1 127 70 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 346 46 1 62 3 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 341 45 1 67 27 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 322 52 12 68 23 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 314 109 61 63 15 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 309 70 21 71 25 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 295 55 12 134 79 NC_009009:SSA_0963|3end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_972890..973040_POSITIVE 292 49 3 71 20 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 288 49 1 60 1 NC_009009:SSA_2000|3end_hypothetical_protein_1996987..1997137_NEGATIVE 288 50 5 62 15 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 288 65 21 45 1 NC_009009:SSA_0316|3end_hypothetical_protein_311342..311492_POSITIVE 286 50 2 53 8 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 286 47 7 40 3 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 286 59 12 51 1 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 286 50 9 142 106 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 285 49 1 67 21 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 283 60 16 47 3 NC_009009:SSA_1257|3end_hypothetical_protein_1283106..1283256_NEGATIVE 279 360 311 150 102 NC_009009:SSA_1841|3end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1834422..1834572_NEGATIVE