Origin IGS: attgctatcgtttggtcaggtaaatatagccgtcttttcaaatcgtcggtcatgattattgccgaaatatataaaagcaatgaggctgtatcaagggatcgaacctcaatgacacagcctcagattgtggaattatctgtcagaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctctgacagataattccacaatctgaggctgtgtcattgaggttcgatcccttgatacagcctcattgcttttatatatttcggcaataatcatgaccgacgatttgaaaagacggctatatttacctgaccaaacgatagcaat Mask Tandem Repeat Region ================================================ attgctatcgtttggtcaggtaaatatagccgtcttttcaaatcgtcggtcatgattattgccgaaatatataaaagcaatgaggctgtatcaagggatcgaacctcaatgacacagcctcagattgtggaattatctgtcagaga Find is-nt database================================================ Query_seq: PG0898:PG0899|PG0898:PG0899:hypothetical protein:cytochrome d ubiquinol oxidase, subunit II:<-<-:963441..963586 146 attgctatcgtttggtcaggtaaatatagccgtcttttcaaatcgtcggtcatgattattgccgaaatatataaaagcaatgaggctgtatcaagggatcgaacctcaatgacacagcctcagattgtggaattatctgtcagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0898:PG0899|PG0898:PG0899:hypothetical protein:cytochrome d ubiquinol oxidase, subunit II:<-<-:963441..963586 146 attgctatcgtttggtcaggtaaatatagccgtcttttcaaatcgtcggtcatgattattgccgaaatatataaaagcaatgaggctgtatcaagggatcgaacctcaatgacacagcctcagattgtggaattatctgtcagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0898:PG0899|PG0898:PG0899:hypothetical protein:cytochrome d ubiquinol oxidase, subunit II:<-<-:963441..963586 146 attgctatcgtttggtcaggtaaatatagccgtcttttcaaatcgtcggtcatgattattgccgaaatatataaaagcaatgaggctgtatcaagggatcgaacctcaatgacacagcctcagattgtggaattatctgtcagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attgctatcgtttggtcaggtaaatatagccgtcttttcaaatcgtcggtcatgattattgccgaaatatataaaagcaatgaggctgtatcaagggatcgaacctcaatgacacagcctcagattgtggaattatctgtcagaga Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 1 End: 144 M A I V W S G K Y S R L F K S S V M I I A E I Y K S N E A V S R D R T S M T Q P Q I V E L S V R .. Protein_Len: 36 Strand: - Start: 3 End: 110 .. A I T Q D P L Y L R R K L D D T M I I A S I Y L L L S A T D L S R V E M .................................... attgctatcgtttggtcaggtaaatatagccgtcttttcaaatcgtcggtcatgattattgccgaaatatataaaagcaatgaggctgtatcaagggatcgaacctcaatgacacagcctcagattgtggaattatctgtcagaga 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: 83 Start: 66 End: 95 .................................................................CTTGATACAGCCTCATTGCTTTTATATATT................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attgctatcgtttggtcaggtaaatatagccgtcttttcaaatcgtcggtcatgattattgccgaaatatataaaagcaatgaggctgtatcaagggatcgaacctcaatgacacagcctcagattgtggaattatctgtcagaga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -8.1 Tail_Score: -3.81672 Start: 81 End: 122 Full_Region: gataattccacaatc tgaggctgtgtcattgaggt tcg atcccttgatacagcctca ttgcttttatatatt ................................................................................tgaggctgtgtcattgaggttcgatcccttgatacagcctca........................ Find igs database================================================ Query_seq: PG0898:PG0899|PG0898:PG0899:hypothetical protein:cytochrome d ubiquinol oxidase, subunit II:<-<-:963441..963586 146 attgctatcgtttggtcaggtaaatatagccgtcttttcaaatcgtcggtcatgattattgccgaaatatataaaagcaatgaggctgtatcaagggatcgaacctcaatgacacagcctcagattgtggaattatctgtcagaga Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: NC_002950_PG0898_PG0899|hypothetical protein:cytochrome d ubiquinol oxidase, subunit II|NEGATIVE:NEGATIVE|[963441,963586]|146 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 attgctatcgtttggtcaggtaaatatagccgtcttttcaaatcgtcggtcatgattattgccgaaatatataaaagcaatgaggctgtatcaagggatcgaacctcaatgacacagcctcagattgtggaattatctgtcagaga attgctatcgtttggtcaggtaaatatagccgtcttttcaaatcgtcggtcatgattattgccgaaatatataaaagcaatgaggctgtatcaagggatcgaacctcaatgacacagcctcagattgtggaattatctgtcagaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGCUAUCGUUUGGUCAGGUAAAUAUAGCCGUCUUUUCAAAUCGUCGGUCAUGAUUAUUGCCGAAAUAUAUAAAAGCAAUGAGGCUGUAUCAAGGGAUCGAACCUCAAUGACACAGCCUCAGAUUGUGGAAUUAUCUGUCAGAGA ..........(((((.(((((((.(((((..(.(((((.......((((.((.......)))))).......))))))..(((((((((.((((((.......)))...))).)))))))))..)))))...)))))))))))).. (-39.74) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCUGACAGAUAAUUCCACAAUCUGAGGCUGUGUCAUUGAGGUUCGAUCCCUUGAUACAGCCUCAUUGCUUUUAUAUAUUUCGGCAAUAAUCAUGACCGACGAUUUGAAAAGACGGCUAUAUUUACCUGACCAAACGAUAGCAAU ..(((..(((((............(((((((((((((..(.((......))).)))))))))))))...............((((((.......)).))))..)))))...)))..(((((.................)))))... (-35.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 994 130 81 221 172 NC_002950:PG0898|5end_hypothetical_protein_963350..963580_NEGATIVE 377 120 76 173 124 NC_002950:PG0757|5end_hypothetical_protein_806370..806600_NEGATIVE 360 64 28 80 35 NC_002950:PG0016|5end_sigma-54_dependent_DNA-binding_response_regulator_16947..17177_POSITIVE 358 125 82 186 143 NC_002950:PG1418|5end_DNA_polymerase_III,_gamma_and_tau_subunits_1503064..1503294_POSITIVE 347 50 8 231 181 NC_002950:PG0841|5end_mobilizable_transposon,_excision_protein,_putative_903674..903904_NEGATIVE 331 50 4 101 39 NC_002950:PG1475|5end_conjugative_transposon_protein_TraN_1551835..1552065_NEGATIVE 327 124 81 190 149 NC_002950:PG1947|5end_TPR_domain_protein_2032932..2033162_POSITIVE 314 99 51 125 73 NC_002950:PG1281|5end_hypothetical_protein_1358848..1359078_POSITIVE 312 89 42 128 90 NC_002950:PG0091|5end_transporter,_putative_107400..107630_NEGATIVE 306 49 1 157 109 NC_002950:PG1571|5end_metallo-beta-lactamase_superfamily_protein_1650353..1650583_NEGATIVE 298 122 81 150 118 NC_002950:PG1088|5end_acetyltransferase,_GNAT_family_1155426..1155656_NEGATIVE 297 45 3 75 27 NC_002950:PG0002|5end_hexapeptide_transferase_family_protein_1295..1525_POSITIVE 287 65 29 111 78 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 287 50 4 72 27 NC_002950:PG0165|5end_heat_shock_protein_15_187807..188037_NEGATIVE 286 119 73 154 109 NC_002950:PG1759|5end_adhesion_protein,_putative_1845570..1845800_POSITIVE 286 128 84 182 138 NC_002950:PG0480|5end_precorrin-2_C20-methyltransferase,_putative_521319..521549_NEGATIVE 283 65 26 165 121 NC_002950:PG0528|5end_amidophosphoribosyltransferase,_putative_572720..572950_POSITIVE 283 120 71 151 110 NC_002950:PG0248|5end_translation_initation_factor_SUI1,_putative_281842..282072_NEGATIVE 282 50 1 102 46 NC_002950:PG1477|5end_hypothetical_protein_1553496..1553726_NEGATIVE 282 63 26 95 55 NC_002950:PG0646|5end_iron_compound_ABC_transporter,_ATP-binding_protein_699071..699301_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 430 127 82 60 20 NC_002950:PG2170|3end_sugar_transporter_2276685..2276835_NEGATIVE 377 120 76 76 27 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE 361 120 75 62 13 NC_002950:PG0548|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_605759..605909_POSITIVE 358 125 82 63 20 NC_002950:PG1417|3end_fumarate_hydratase_class_I,_anaerobic_1503021..1503171_POSITIVE 347 50 8 95 45 NC_002950:PG0842|3end_mobilizable_transposon,_hypothetical_protein,_putative_903810..903960_NEGATIVE 341 128 83 62 19 NC_002950:PG0395|3end_DNA-directed_RNA_polymerase_beta'_subunit_433305..433455_POSITIVE 331 50 4 78 16 NC_002950:PG1476|3end_conjugative_transposon_protein_TraM_1551858..1552008_NEGATIVE 318 130 85 102 56 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 314 118 76 135 89 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 314 123 81 62 33 NC_002950:PG0694|3end_immunoreactive_42_kDa_antigen_PG33_749703..749853_NEGATIVE 312 89 42 69 31 NC_002950:PG0092|3end_transporter,_putative_107459..107609_NEGATIVE 311 130 84 79 31 NC_002950:PG0350|3end_internalin-related_protein_385356..385506_NEGATIVE 308 124 84 44 9 NC_002950:PG1950|3end_hypothetical_protein_2040840..2040990_POSITIVE 306 49 1 64 16 NC_002950:PG1572|3end_hypothetical_protein_1650446..1650596_NEGATIVE 302 47 1 92 41 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 301 121 82 63 24 NC_002950:PG0159|3end_endopeptidase_PepO_181095..181245_NEGATIVE 298 122 81 53 21 NC_002950:PG1089|3end_DNA-binding_response_regulator_RprY_1155523..1155673_NEGATIVE 297 119 76 59 16 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 297 45 3 62 14 NC_002950:PG0001|3end_chromosomal_replication_initiation_protein_1362..1512_POSITIVE 296 121 82 63 24 NC_002950:PG1847|3end_endoribonuclease_L-PSP,_putative_1946227..1946377_NEGATIVE