Origin IGS: cacacgtagctttctgctctgtcatttgaggaaataatagttgtcaatctggcgatcgcagtagctgcaagatttttgaaatataatctagcaaggggaagtggacggactgaaatcaaggatttccgagtccggtcactcccttattttgtaggtggttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaccacctacaaaataagggagtgaccggactcggaaatccttgatttcagtccgtccacttccccttgctagattatatttcaaaaatcttgcagctactgcgatcgccagattgacaactattatttcctcaaatgacagagcagaaagctacgtgtg Mask Tandem Repeat Region ================================================ cacacgtagctttctgctctgtcatttgaggaaataatagttgtcaatctggcgatcgcagtagctgcaagatttttgaaatataatctagcaaggggaagtggacggactgaaatcaaggatttccgagtccggtcactcccttattttgtaggtggttt Find is-nt database================================================ Query_seq: SSA_0966:SSA_0967|SSA_0966:SSA_0967:Uridine kinase, putative:hypothetical protein:->->:975851..976011 161 cacacgtagctttctgctctgtcatttgaggaaataatagttgtcaatctggcgatcgcagtagctgcaagatttttgaaatataatctagcaaggggaagtggacggactgaaatcaaggatttccgagtccggtcactcccttattttgtaggtggttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0966:SSA_0967|SSA_0966:SSA_0967:Uridine kinase, putative:hypothetical protein:->->:975851..976011 161 cacacgtagctttctgctctgtcatttgaggaaataatagttgtcaatctggcgatcgcagtagctgcaagatttttgaaatataatctagcaaggggaagtggacggactgaaatcaaggatttccgagtccggtcactcccttattttgtaggtggttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0966:SSA_0967|SSA_0966:SSA_0967:Uridine kinase, putative:hypothetical protein:->->:975851..976011 161 cacacgtagctttctgctctgtcatttgaggaaataatagttgtcaatctggcgatcgcagtagctgcaagatttttgaaatataatctagcaaggggaagtggacggactgaaatcaaggatttccgagtccggtcactcccttattttgtaggtggttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cacacgtagctttctgctctgtcatttgaggaaataatagttgtcaatctggcgatcgcagtagctgcaagatttttgaaatataatctagcaaggggaagtggacggactgaaatcaaggatttccgagtccggtcactcccttattttgtaggtggttt Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 19 End: 159 .................. M S F E E I I V V N L A I A V A A R F L K Y N L A R G S G R T E I K D F R V R S L P Y F V G G .. Protein_Len: 39 Strand: - Start: 3 End: 119 .. V Y S E A R D N S S I I T T L R A I A T A A L N K F Y L R A L P L P R V S I M .......................................... cacacgtagctttctgctctgtcatttgaggaaataatagttgtcaatctggcgatcgcagtagctgcaagatttttgaaatataatctagcaaggggaagtggacggactgaaatcaaggatttccgagtccggtcactcccttattttgtaggtggttt 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================================================ cacacgtagctttctgctctgtcatttgaggaaataatagttgtcaatctggcgatcgcagtagctgcaagatttttgaaatataatctagcaaggggaagtggacggactgaaatcaaggatttccgagtccggtcactcccttattttgtaggtggttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -8.9 Tail_Score: -4.33182 Start: 97 End: 143 Full_Region: TATAATCTAGCAAGG GGAAGTGGACGGACTGAAATC AAG GATTTCCGAGTCCGGTCACTCCC TTATTTTGTAGGTGG ................................................................................................GGAAGTGGACGGACTGAAATCAAGGATTTCCGAGTCCGGTCACTCCC.................. Find igs database================================================ Query_seq: SSA_0966:SSA_0967|SSA_0966:SSA_0967:Uridine kinase, putative:hypothetical protein:->->:975851..976011 161 cacacgtagctttctgctctgtcatttgaggaaataatagttgtcaatctggcgatcgcagtagctgcaagatttttgaaatataatctagcaaggggaagtggacggactgaaatcaaggatttccgagtccggtcactcccttattttgtaggtggttt Intra-Species Hit: Count: 1 Min: 1 Max: 161 Len: 161 Subject: NC_009009_SSA_0966_SSA_0967|Uridine kinase, putative:hypothetical protein|POSITIVE:POSITIVE|[975851,976011]|161 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 161 Query Start:1 Query End:161 Subject Strand: POSITIVE Subject Start: 1 Subject End: 161 cacacgtagctttctgctctgtcatttgaggaaataatagttgtcaatctggcgatcgcagtagctgcaagatttttgaaatataatctagcaaggggaagtggacggactgaaatcaaggatttccgagtccggtcactcccttattttgtaggtggttt cacacgtagctttctgctctgtcatttgaggaaataatagttgtcaatctggcgatcgcagtagctgcaagatttttgaaatataatctagcaaggggaagtggacggactgaaatcaaggatttccgagtccggtcactcccttattttgtaggtggttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACACGUAGCUUUCUGCUCUGUCAUUUGAGGAAAUAAUAGUUGUCAAUCUGGCGAUCGCAGUAGCUGCAAGAUUUUUGAAAUAUAAUCUAGCAAGGGGAAGUGGACGGACUGAAAUCAAGGAUUUCCGAGUCCGGUCACUCCCUUAUUUUGUAGGUGGUUU (((..((((((..((((..(((((.((((.((........)).))))..)))))...)))).)))))).(((((..........)))))....((((((.(((..((((((((((((...))))))..))))))..))))))))).........))).... (-52.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACCACCUACAAAAUAAGGGAGUGACCGGACUCGGAAAUCCUUGAUUUCAGUCCGUCCACUUCCCCUUGCUAGAUUAUAUUUCAAAAAUCUUGCAGCUACUGCGAUCGCCAGAUUGACAACUAUUAUUUCCUCAAAUGACAGAGCAGAAAGCUACGUGUG ....(((...........(((((((..((((((..((((((...))))))))))))..)))))))...(((.(((((..........))))).)))(((.((((((((....)))).....((.((((((....)))))).)).))))..)))...))).. (-40.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 80 43 75 37 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 354 58 11 74 29 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 340 139 93 166 112 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 337 142 109 222 190 NC_009009:SSA_0997|5end_DNA-directed_DNA_polymerase_III_chain,_putative_996779..997009_POSITIVE 324 75 36 231 184 NC_009009:SSA_0284|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIC_component,_putative_274888..275118_POSITIVE 323 138 93 171 117 NC_009009:SSA_1511|5end_Glycosyltransferase,_putative_1516697..1516927_NEGATIVE 320 160 117 225 180 NC_009009:SSA_0151|5end_hypothetical_protein_145354..145584_POSITIVE 312 77 39 41 7 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 308 59 11 218 156 NC_009009:SSA_0376|5end_ABC-type_methionine_transporter,_ATPase_component,_putative_365379..365609_POSITIVE 302 160 117 167 125 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 300 78 41 214 172 NC_009009:SSA_1944|5end_Oligopeptide_transport_ATP-binding_protein,_putative_1936611..1936841_NEGATIVE 299 140 94 115 65 NC_009009:SSA_0800|5end_Glutamine_amidotransferase,_putative_782774..783004_NEGATIVE 297 143 101 229 183 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 293 158 120 49 5 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 292 140 91 61 10 NC_009009:SSA_0833|5end_Accessory_secretory_protein_Asp1,_putative_817940..818170_POSITIVE 287 68 28 69 22 NC_009009:SSA_1469|5end_Shikimate_dehydrogenase,_putative_1476317..1476547_NEGATIVE 285 138 91 59 18 NC_009009:SSA_1971|5end_hypothetical_protein_1967167..1967397_POSITIVE 282 160 112 59 2 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 281 116 71 174 122 NC_009009:SSA_1055|5end_Conserved_uncharacterized_protein_1070899..1071129_POSITIVE 280 138 91 180 136 NC_009009:SSA_1239|5end_hypothetical_protein_1264689..1264919_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 58 11 77 32 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 312 77 39 39 5 NC_009009:SSA_1415|3end_Oxidoreductase,_putative_1425414..1425564_NEGATIVE 299 140 94 115 65 NC_009009:SSA_0801|3end_Mur_ligase_family_protein,_putative_782774..782924_NEGATIVE 292 140 91 52 1 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 292 143 102 151 111 NC_009009:SSA_0243|3end_Cyclo-nucleotide_phosphodiesterase,_putative_235824..235974_NEGATIVE 291 136 91 48 6 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 290 150 101 77 27 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE 287 68 28 79 32 NC_009009:SSA_1470|3end_3-dehydroquinate_dehydratase,_putative_1476307..1476457_NEGATIVE 280 138 91 68 24 NC_009009:SSA_1240|3end_Orotate_phosphoribosyltransferase,_putative_1264801..1264951_NEGATIVE 278 80 49 33 1 NC_009009:SSA_1956|3end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1952644..1952794_NEGATIVE 278 160 124 52 1 NC_009009:SSA_1047|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_1062845..1062995_POSITIVE 278 140 95 77 24 NC_009009:SSA_0570|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_565461..565611_POSITIVE 275 160 115 73 28 NC_009009:SSA_0287|3end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_280702..280852_POSITIVE 270 138 100 37 3 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 265 59 11 125 76 NC_009009:SSA_2208|3end_Preprotein_translocase_secE_component,_putative_2207734..2207884_NEGATIVE 265 153 115 48 7 NC_009009:SSA_1710|3end_Transcriptional_regulator,_XRE_family,_putative_1699011..1699161_POSITIVE 263 137 94 127 78 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 263 68 25 141 90 NC_009009:SSA_1640|3end_hypothetical_protein_1642108..1642258_NEGATIVE 259 137 95 91 51 NC_009009:SSA_2081|3end_hypothetical_protein_2085490..2085640_POSITIVE 258 29 5 145 118 NC_009009:SSA_1786|3end_Conserved_uncharacterized_protein_1769996..1770146_NEGATIVE