Origin IGS: ggcaggactatcggtattatgtcgaatagttttgttcggtcagctgcgcgagaaagggaatgactctccggcaactctattccgagcagactattctctatgttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaacatagagaatagtctgctcggaatagagttgccggagagtcattccctttctcgcgcagctgaccgaacaaaactattcgacataataccgatagtcctgcc Mask Tandem Repeat Region ================================================ ggcaggactatcggtattatgtcgaatagttttgttcggtcagctgcgcgagaaagggaatgactctccggcaactctattccgagcagactattctctatgttt Find is-nt database================================================ Query_seq: PG2096:PG2097|PG2096:PG2097:hypothetical protein:ribose-phosphate pyrophosphokinase:<-<-:2205506..2205610 105 ggcaggactatcggtattatgtcgaatagttttgttcggtcagctgcgcgagaaagggaatgactctccggcaactctattccgagcagactattctctatgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2096:PG2097|PG2096:PG2097:hypothetical protein:ribose-phosphate pyrophosphokinase:<-<-:2205506..2205610 105 ggcaggactatcggtattatgtcgaatagttttgttcggtcagctgcgcgagaaagggaatgactctccggcaactctattccgagcagactattctctatgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2096:PG2097|PG2096:PG2097:hypothetical protein:ribose-phosphate pyrophosphokinase:<-<-:2205506..2205610 105 ggcaggactatcggtattatgtcgaatagttttgttcggtcagctgcgcgagaaagggaatgactctccggcaactctattccgagcagactattctctatgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggcaggactatcggtattatgtcgaatagttttgttcggtcagctgcgcgagaaagggaatgactctccggcaactctattccgagcagactattctctatgttt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 3 End: 101 .. L V I P I I D F L K T R D A A R S L S H S E P L E I G L L S N E M .... ggcaggactatcggtattatgtcgaatagttttgttcggtcagctgcgcgagaaagggaatgactctccggcaactctattccgagcagactattctctatgttt 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================================================ ggcaggactatcggtattatgtcgaatagttttgttcggtcagctgcgcgagaaagggaatgactctccggcaactctattccgagcagactattctctatgttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2096:PG2097|PG2096:PG2097:hypothetical protein:ribose-phosphate pyrophosphokinase:<-<-:2205506..2205610 105 ggcaggactatcggtattatgtcgaatagttttgttcggtcagctgcgcgagaaagggaatgactctccggcaactctattccgagcagactattctctatgttt Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_002950_PG2096_PG2097|hypothetical protein:ribose-phosphate pyrophosphokinase|NEGATIVE:NEGATIVE|[2205506, 2205610]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 ggcaggactatcggtattatgtcgaatagttttgttcggtcagctgcgcgagaaagggaatgactctccggcaactctattccgagcagactattctctatgttt ggcaggactatcggtattatgtcgaatagttttgttcggtcagctgcgcgagaaagggaatgactctccggcaactctattccgagcagactattctctatgttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCAGGACUAUCGGUAUUAUGUCGAAUAGUUUUGUUCGGUCAGCUGCGCGAGAAAGGGAAUGACUCUCCGGCAACUCUAUUCCGAGCAGACUAUUCUCUAUGUUU ((((..((.....))....))))(((((((((.((((((..((.(((.((.((.((.......)).))))))).)).....)))))))))))))))......... (-28.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACAUAGAGAAUAGUCUGCUCGGAAUAGAGUUGCCGGAGAGUCAUUCCCUUUCUCGCGCAGCUGACCGAACAAAACUAUUCGACAUAAUACCGAUAGUCCUGCC .........(((((((.((.((((.....(((((((((((((.......))))).)).))))))..)))).))..)))))))....................... (-26.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1068 90 41 181 132 NC_002950:PG2096|5end_hypothetical_protein_2205415..2205645_NEGATIVE 403 86 41 55 4 NC_002950:PG2205|5end_2-dehydropantoate_2-reductase_2316121..2316351_POSITIVE 396 90 41 62 7 NC_002950:PG2110|5end_thiamine_biosynthesis_protein_ThiC_2221212..2221442_NEGATIVE 378 70 22 60 15 NC_002950:PG0357|5end_aspartate_carbamoyltransferase_catalytic_subunit_391440..391670_POSITIVE 370 88 43 192 135 NC_002950:PG1479|5end_conjugative_transposon_protein_TraJ_1555234..1555464_NEGATIVE 369 70 21 63 6 NC_002950:PG0751|5end_porT_protein_797578..797808_NEGATIVE 369 90 42 166 113 NC_002950:PG0140|5end_hypothetical_protein_163858..164088_NEGATIVE 360 80 34 49 6 NC_002950:PG1063|5end_transcriptional_regulator,_putative_1131056..1131286_POSITIVE 360 74 33 69 28 NC_002950:PG0369|5end_phosphopantetheine_adenylyltransferase_403210..403440_POSITIVE 354 76 31 56 3 NC_002950:PG0033|5end_RmuC_domain_protein_41540..41770_NEGATIVE 351 88 41 208 158 NC_002950:PG0558|5end_purine_nucleoside_phosphorylase_616331..616561_NEGATIVE 349 48 1 207 153 NC_002950:PG0364|5end_hypothetical_protein_399615..399845_NEGATIVE 346 86 42 215 169 NC_002950:PG2090|5end_cation_efflux_family_protein_2190230..2190460_POSITIVE 344 66 21 137 82 NC_002950:PG0952|5end_4-hydroxy-3-methylbut-2-en-1-yl_diphosphate_synthase_1010922..1011152_POSITIVE 344 80 38 64 20 NC_002950:PG0776|5end_electron_transfer_flavoprotein,_alpha_subunit_830184..830414_NEGATIVE 343 72 37 70 32 NC_002950:PG0146|5end_hypothetical_protein_169115..169345_NEGATIVE 341 48 1 46 2 NC_002950:PG0444|5end_oligopeptide_transporter,_OPT_family_483256..483486_POSITIVE 340 90 46 53 11 NC_002950:PG0195|5end_rubrerythrin_232046..232276_POSITIVE 337 60 11 75 21 NC_002950:PG1725|5end_competence/damage-inducible_protein_CinA_domain_protein_1814766..1814996_POSITIVE 337 85 42 67 23 NC_002950:PG0793|5end_fructose-1,6-bisphosphatase_844288..844518_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 426 99 55 87 41 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE 372 72 38 119 89 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 369 90 42 146 93 NC_002950:PG0141|3end_spoOJ_protein_163878..164028_NEGATIVE 360 87 41 98 45 NC_002950:PG1338|3end_umuC_protein_1419624..1419774_POSITIVE 360 78 38 59 18 NC_002950:PG0231|3end_hypothetical_protein_267409..267559_POSITIVE 349 50 2 129 75 NC_002950:PG0656|3end_50S_ribosomal_protein_L34_706945..707095_NEGATIVE 344 80 38 55 11 NC_002950:PG0777|3end_electron_transfer_flavoprotein,_beta_subunit_830193..830343_NEGATIVE 343 72 37 57 19 NC_002950:PG0147|3end_hypothetical_protein_169128..169278_NEGATIVE 342 77 35 85 42 NC_002950:PG0381|3end_cell_volume_regulation_protein_CvrA_411185..411335_NEGATIVE 337 49 1 137 71 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 337 60 11 75 21 NC_002950:PG1724|3end_O-sialoglycoprotein_endopeptidase_1814846..1814996_POSITIVE 332 47 1 124 78 NC_002950:PG1246|3end_alanyl-tRNA_synthetase_1324509..1324659_POSITIVE 326 88 43 86 52 NC_002950:PG1215|3end_lipoprotein_protein,_putative_1295513..1295663_POSITIVE 322 89 47 54 1 NC_002950:PG0085|3end_alpha-galactosidase_100556..100706_POSITIVE 320 49 2 84 29 NC_002950:PG1486|3end_conjugative_transposon_protein_TraA_1560357..1560507_NEGATIVE 316 90 42 83 22 NC_002950:PG0232|3end_zinc_carboxypeptidase,_putative_267458..267608_NEGATIVE 313 48 2 138 86 NC_002950:PG1977|3end_hypothetical_protein_2064687..2064837_NEGATIVE 312 78 37 148 101 NC_002950:PG1480|3end_conjugative_transposon_protein_TraI_1555266..1555416_NEGATIVE 312 48 2 109 64 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE 311 72 35 147 114 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE