Origin IGS: ttctcgcagagtgcctcaaagagcatttgcctgaataaaaaagttgtctacgggctgtgtcgaataagggtgaaaccttaggacacagcctttctttttggtagatttgcaatct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agattgcaaatctaccaaaaagaaaggctgtgtcctaaggtttcacccttattcgacacagcccgtagacaacttttttattcaggcaaatgctctttgaggcactctgcgagaa Mask Tandem Repeat Region ================================================ ttctcgcagagtgcctcaaagagcatttgcctgaataaaaaagttgtctacgggctgtgtcgaataagggtgaaaccttaggacacagcctttctttttggtagatttgcaatct Find is-nt database================================================ Query_seq: PG1758:PG1759|PG1758:PG1759:ribosomal protein S15:adhesion protein, putative:->->:1845595..1845709 115 ttctcgcagagtgcctcaaagagcatttgcctgaataaaaaagttgtctacgggctgtgtcgaataagggtgaaaccttaggacacagcctttctttttggtagatttgcaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1758:PG1759|PG1758:PG1759:ribosomal protein S15:adhesion protein, putative:->->:1845595..1845709 115 ttctcgcagagtgcctcaaagagcatttgcctgaataaaaaagttgtctacgggctgtgtcgaataagggtgaaaccttaggacacagcctttctttttggtagatttgcaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1758:PG1759|PG1758:PG1759:ribosomal protein S15:adhesion protein, putative:->->:1845595..1845709 115 ttctcgcagagtgcctcaaagagcatttgcctgaataaaaaagttgtctacgggctgtgtcgaataagggtgaaaccttaggacacagcctttctttttggtagatttgcaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctcgcagagtgcctcaaagagcatttgcctgaataaaaaagttgtctacgggctgtgtcgaataagggtgaaaccttaggacacagcctttctttttggtagatttgcaatct Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 2 End: 112 . R A S H R L S C K G S Y F L Q R R A T D F L P S V K P C L R E K Q Y I Q M ... ttctcgcagagtgcctcaaagagcatttgcctgaataaaaaagttgtctacgggctgtgtcgaataagggtgaaaccttaggacacagcctttctttttggtagatttgcaatct 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================================================ ttctcgcagagtgcctcaaagagcatttgcctgaataaaaaagttgtctacgggctgtgtcgaataagggtgaaaccttaggacacagcctttctttttggtagatttgcaatct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -4.3 Tail_Score: -4.91852 Start: 53 End: 90 Full_Region: AAAAAGTTGTCTACG GGCTGTGTCGAATAAGG GTGAAA CCTTAGGACACAGCC TTTCTTTTTGGTAGA ....................................................GGCTGTGTCGAATAAGGGTGAAACCTTAGGACACAGCC......................... Find igs database================================================ Query_seq: PG1758:PG1759|PG1758:PG1759:ribosomal protein S15:adhesion protein, putative:->->:1845595..1845709 115 ttctcgcagagtgcctcaaagagcatttgcctgaataaaaaagttgtctacgggctgtgtcgaataagggtgaaaccttaggacacagcctttctttttggtagatttgcaatct Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_002950_PG1758_PG1759|ribosomal protein S15:adhesion protein, putative|POSITIVE:POSITIVE|[1845595,1845709]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 ttctcgcagagtgcctcaaagagcatttgcctgaataaaaaagttgtctacgggctgtgtcgaataagggtgaaaccttaggacacagcctttctttttggtagatttgcaatct ttctcgcagagtgcctcaaagagcatttgcctgaataaaaaagttgtctacgggctgtgtcgaataagggtgaaaccttaggacacagcctttctttttggtagatttgcaatct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUCGCAGAGUGCCUCAAAGAGCAUUUGCCUGAAUAAAAAAGUUGUCUACGGGCUGUGUCGAAUAAGGGUGAAACCUUAGGACACAGCCUUUCUUUUUGGUAGAUUUGCAAUCU (((..(((((.((((.....).))))))))..))).......((.((((((((((((((((...(((((......))))).)))))))))).........))))))..))..... (-38.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUGCAAAUCUACCAAAAAGAAAGGCUGUGUCCUAAGGUUUCACCCUUAUUCGACACAGCCCGUAGACAACUUUUUUAUUCAGGCAAAUGCUCUUUGAGGCACUCUGCGAGAA (((.(((...(((((..........(((((((((.(((((......)))))...))))))))).)))))............((((((....)))...))).))).)))....... (-30.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 91 52 211 173 NC_002950:PG0898|5end_hypothetical_protein_963350..963580_NEGATIVE 366 100 52 228 176 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 332 69 23 57 12 NC_002950:PG1611|5end_hypothetical_protein_1691487..1691717_NEGATIVE 325 72 31 41 1 NC_002950:PG0711|5end_hypothetical_protein_766070..766300_POSITIVE 315 90 46 189 150 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 308 59 13 100 41 NC_002950:PG1725|5end_competence/damage-inducible_protein_CinA_domain_protein_1814766..1814996_POSITIVE 304 82 51 66 42 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 303 91 51 180 141 NC_002950:PG1418|5end_DNA_polymerase_III,_gamma_and_tau_subunits_1503064..1503294_POSITIVE 297 89 46 125 79 NC_002950:PG0508|5end_HAD-superfamily_subfamily_IB_hydrolase,_TIGR01490_548738..548968_NEGATIVE 295 95 52 178 130 NC_002950:PG0757|5end_hypothetical_protein_806370..806600_NEGATIVE 287 89 47 167 127 NC_002950:PG1760|5end_ABC_transporter,_ATP-binding_protein_1846507..1846737_POSITIVE 286 89 41 67 19 NC_002950:PG0511|5end_spore_maturation_protein_A/spore_maturation_protein_B_551328..551558_NEGATIVE 285 90 52 224 193 NC_002950:PG0749|5end_hypothetical_protein_795654..795884_NEGATIVE 283 69 26 183 144 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 283 100 52 210 152 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 282 59 17 53 4 NC_002950:PG0462|5end_transporter,_putative_506279..506509_NEGATIVE 278 57 12 138 82 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 278 34 1 151 114 NC_002950:PG0713|5end_anthranilate_synthase_component_II_767749..767979_NEGATIVE 276 90 43 52 7 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 275 88 50 149 112 NC_002950:PG2002|5end_dihydrodipicolinate_reductase_2091587..2091817_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 447 100 52 60 15 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 440 93 52 69 35 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 415 100 51 70 20 NC_002950:PG0548|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_605759..605909_POSITIVE 415 99 52 66 19 NC_002950:PG0349|3end_hydrolase,_haloacid_dehalogenase-like_family_385291..385441_POSITIVE 399 91 52 64 26 NC_002950:PG0899|3end_cytochrome_d_ubiquinol_oxidase,_subunit_II_963497..963647_NEGATIVE 390 90 41 55 7 NC_002950:PG2010|3end_phosphomannomutase,_putative_2100952..2101102_POSITIVE 386 109 67 46 2 NC_002950:PG1755|3end_fructose-bisphosphate_aldolase_1842397..1842547_NEGATIVE 374 97 52 50 10 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 366 100 52 81 29 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 365 97 52 92 51 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 359 92 52 56 20 NC_002950:PG0395|3end_DNA-directed_RNA_polymerase_beta'_subunit_433305..433455_POSITIVE 355 96 52 43 7 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 348 90 53 38 1 NC_002950:PG1758|3end_ribosomal_protein_S15_1845534..1845684_POSITIVE 328 93 52 60 21 NC_002950:PG0779|3end_hypothetical_protein_832100..832250_NEGATIVE 323 94 52 65 24 NC_002950:PG1847|3end_endoribonuclease_L-PSP,_putative_1946227..1946377_NEGATIVE 322 98 52 69 28 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 308 59 13 100 41 NC_002950:PG1724|3end_O-sialoglycoprotein_endopeptidase_1814846..1814996_POSITIVE 303 91 51 57 18 NC_002950:PG1417|3end_fumarate_hydratase_class_I,_anaerobic_1503021..1503171_POSITIVE 303 93 51 51 8 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 302 98 54 42 1 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE