Origin IGS: tatgaaatttcggcgaaaaaattactcgctgcaagcttgcggccattaatctcggaagcaaaatttgtcactgcaagcatgtaacagtattttctgcaaccgaaatcaccgtctgcaaacttgaatcaaagagatactaatcataagacaattattttctcaataaaataatcattacttccatatttagtcatagctatc .........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 gatagctatgactaaatatggaagtaatgattattttattgagaaaataattgtcttatgattagtatctctttgattcaagtttgcagacggtgatttcggttgcagaaaatactgttacatgcttgcagtgacaaattttgcttccgagattaatggccgcaagcttgcagcgagtaattttttcgccgaaatttcata Mask Tandem Repeat Region ================================================ tatgaaatttcggcgaaaaaattactcgctgcaagcttgcggccattaatctcggaagcaaaatttgtcactgcaagcatgtaacagtattttctgcaaccgaaatcaccgtctgcaaacttgaatcaaagagatactaatcataagacaattattttctcaataaaataatcattacttccatatttagtcatagctatc Find is-nt database================================================ Query_seq: PG0681:PG0682|PG0681:PG0682:hypothetical protein:ABC transporter, permease protein, putative:<-->:732810..733010 201 tatgaaatttcggcgaaaaaattactcgctgcaagcttgcggccattaatctcggaagcaaaatttgtcactgcaagcatgtaacagtattttctgcaaccgaaatcaccgtctgcaaacttgaatcaaagagatactaatcataagacaattattttctcaataaaataatcattacttccatatttagtcatagctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0681:PG0682|PG0681:PG0682:hypothetical protein:ABC transporter, permease protein, putative:<-->:732810..733010 201 tatgaaatttcggcgaaaaaattactcgctgcaagcttgcggccattaatctcggaagcaaaatttgtcactgcaagcatgtaacagtattttctgcaaccgaaatcaccgtctgcaaacttgaatcaaagagatactaatcataagacaattattttctcaataaaataatcattacttccatatttagtcatagctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0681:PG0682|PG0681:PG0682:hypothetical protein:ABC transporter, permease protein, putative:<-->:732810..733010 201 tatgaaatttcggcgaaaaaattactcgctgcaagcttgcggccattaatctcggaagcaaaatttgtcactgcaagcatgtaacagtattttctgcaaccgaaatcaccgtctgcaaacttgaatcaaagagatactaatcataagacaattattttctcaataaaataatcattacttccatatttagtcatagctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatgaaatttcggcgaaaaaattactcgctgcaagcttgcggccattaatctcggaagcaaaatttgtcactgcaagcatgtaacagtattttctgcaaccgaaatcaccgtctgcaaacttgaatcaaagagatactaatcataagacaattattttctcaataaaataatcattacttccatatttagtcatagctatc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 21 End: 137 .................... M T R C K L A A I N L G S K I C H C K H V T V F S A T E I T V C K L E S K R Y ................................................................ tatgaaatttcggcgaaaaaattactcgctgcaagcttgcggccattaatctcggaagcaaaatttgtcactgcaagcatgtaacagtattttctgcaaccgaaatcaccgtctgcaaacttgaatcaaagagatactaatcataagacaattattttctcaataaaataatcattacttccatatttagtcatagctatc 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================================================ tatgaaatttcggcgaaaaaattactcgctgcaagcttgcggccattaatctcggaagcaaaatttgtcactgcaagcatgtaacagtattttctgcaaccgaaatcaccgtctgcaaacttgaatcaaagagatactaatcataagacaattattttctcaataaaataatcattacttccatatttagtcatagctatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0681:PG0682|PG0681:PG0682:hypothetical protein:ABC transporter, permease protein, putative:<-->:732810..733010 201 tatgaaatttcggcgaaaaaattactcgctgcaagcttgcggccattaatctcggaagcaaaatttgtcactgcaagcatgtaacagtattttctgcaaccgaaatcaccgtctgcaaacttgaatcaaagagatactaatcataagacaattattttctcaataaaataatcattacttccatatttagtcatagctatc Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: NC_002950_PG0681_PG0682|hypothetical protein:ABC transporter, permease protein, putative|NEGATIVE:POSITIVE|[732810,733010]|201 HSP 1 e-value: 1.0E-110 bit: 398.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 tatgaaatttcggcgaaaaaattactcgctgcaagcttgcggccattaatctcggaagcaaaatttgtcactgcaagcatgtaacagtattttctgcaaccgaaatcaccgtctgcaaacttgaatcaaagagatactaatcataagacaattattttctcaataaaataatcattacttccatatttagtcatagctatc tatgaaatttcggcgaaaaaattactcgctgcaagcttgcggccattaatctcggaagcaaaatttgtcactgcaagcatgtaacagtattttctgcaaccgaaatcaccgtctgcaaacttgaatcaaagagatactaatcataagacaattattttctcaataaaataatcattacttccatatttagtcatagctatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGAAAUUUCGGCGAAAAAAUUACUCGCUGCAAGCUUGCGGCCAUUAAUCUCGGAAGCAAAAUUUGUCACUGCAAGCAUGUAACAGUAUUUUCUGCAACCGAAAUCACCGUCUGCAAACUUGAAUCAAAGAGAUACUAAUCAUAAGACAAUUAUUUUCUCAAUAAAAUAAUCAUUACUUCCAUAUUUAGUCAUAGCUAUC (((((.(((((((.(((((...((((.(.((((.((((((((.((.......(....).......))...)))))))).)))).)))))))))).....)))))))....((((.....(((......))).(((....)))...)))).((((((((......))))))))..................)))))...... (-35.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAGCUAUGACUAAAUAUGGAAGUAAUGAUUAUUUUAUUGAGAAAAUAAUUGUCUUAUGAUUAGUAUCUCUUUGAUUCAAGUUUGCAGACGGUGAUUUCGGUUGCAGAAAAUACUGUUACAUGCUUGCAGUGACAAAUUUUGCUUCCGAGAUUAAUGGCCGCAAGCUUGCAGCGAGUAAUUUUUUCGCCGAAAUUUCAUA ................(((((((............(((..((((...((((..(...)..))))...))))..)))..(((((((((.(.((.(((((((((..((((((.....((((((.((....))))))))..))))))..))))))))).)).).)))))))))..(((((.......))))).....))))))) (-51.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 993 60 11 151 102 NC_002950:PG0681|5end_hypothetical_protein_732719..732949_NEGATIVE 487 68 21 91 44 NC_002950:PG0297|5end_hypothetical_protein_335518..335748_NEGATIVE 334 70 29 56 16 NC_002950:PG2163|5end_acid_phosphatase_2269571..2269801_NEGATIVE 327 57 11 183 130 NC_002950:PG0724|5end_prolyl_oligopeptidase_family_protein_775229..775459_POSITIVE 314 59 11 142 89 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 312 69 21 225 171 NC_002950:PG2099|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2207932..2208162_NEGATIVE 301 65 26 104 62 NC_002950:PG0156|5end_modification_methylase,_HemK_family_178828..179058_POSITIVE 300 58 11 105 47 NC_002950:PG0562|5end_potassium_uptake_protein_TrkA,_putative_619222..619452_POSITIVE 299 60 25 56 19 NC_002950:PG2209|5end_hypothetical_protein_2320928..2321158_NEGATIVE 294 47 2 219 174 NC_002950:PG1042|5end_glycogen_synthase,_putative_1110638..1110868_NEGATIVE 293 117 73 227 187 NC_002950:PG1881|5end_hypothetical_protein_1976524..1976754_POSITIVE 293 60 11 222 165 NC_002950:PG1057|5end_hypothetical_protein_1123419..1123649_POSITIVE 291 78 31 207 146 NC_002950:PG2155|5end_lipoprotein,_putative_2261862..2262092_NEGATIVE 291 69 22 158 106 NC_002950:PG1248|5end_hypothetical_protein_1326532..1326762_NEGATIVE 291 79 31 146 93 NC_002950:PG0242|5end_conserved_hypothetical_protein_TIGR00096_278960..279190_NEGATIVE 289 97 51 207 157 NC_002950:PG1076|5end_acyl-CoA_dehydrogenase,_short-chain_specific_1143485..1143715_POSITIVE 289 60 11 77 13 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 287 59 11 196 145 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 287 56 11 64 19 NC_002950:PG0052|5end_sensor_histidine_kinase_63419..63649_POSITIVE 286 57 11 192 131 NC_002950:PG1855|5end_carboxyl-terminal_protease_1955476..1955706_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 482 59 11 124 79 NC_002950:PG0681|3end_hypothetical_protein_732411..732561_NEGATIVE 452 60 11 129 83 NC_002950:PG0442|3end_hypothetical_protein_481514..481664_NEGATIVE 367 60 12 131 83 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 338 69 25 69 25 NC_002950:PG1881|3end_hypothetical_protein_1978046..1978196_POSITIVE 334 70 29 59 19 NC_002950:PG2164|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2269568..2269718_NEGATIVE 304 59 11 91 42 NC_002950:PG0320|3end_hypothetical_protein_354577..354727_POSITIVE 291 69 22 143 91 NC_002950:PG1249|3end_1-acyl-sn-glycerol-3-phosphate_acetyltransferase,_putative_1326547..1326697_NEGATIVE 291 79 31 130 77 NC_002950:PG0243|3end_hypothetical_protein_278976..279126_NEGATIVE 289 44 9 56 17 NC_002950:PG1410|3end_hypothetical_protein_1493436..1493586_POSITIVE 289 60 11 73 9 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 286 117 72 140 98 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 285 116 71 89 42 NC_002950:PG1826|3end_hypothetical_protein_1919646..1919796_NEGATIVE 285 60 13 71 20 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 282 60 12 117 70 NC_002950:PG0744|3end_RNA_methyltransferase,_TrmH_family_791133..791283_NEGATIVE 282 58 11 71 12 NC_002950:PG0302|3end_hypothetical_protein_338721..338871_POSITIVE 279 72 31 48 9 NC_002950:PG2206|3end_ABC_transporter,_ATP-binding_protein_2317250..2317400_NEGATIVE 278 56 11 147 102 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 277 74 31 64 27 NC_002950:PG1739|3end_hypothetical_protein_1825128..1825278_NEGATIVE 276 126 88 88 50 NC_002950:PG1522|3end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1599100..1599250_NEGATIVE 276 50 10 55 5 NC_002950:PG1246|3end_alanyl-tRNA_synthetase_1324509..1324659_POSITIVE