Origin IGS: ggacgggcggatatgcaatgagacaatcaagcaattaagttacgagagcacttatcgagaagaaggacttgccgatttctcgatgagtgctctttctttttccacccaagcaaattg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caatttgcttgggtggaaaaagaaagagcactcatcgagaaatcggcaagtccttcttctcgataagtgctctcgtaacttaattgcttgattgtctcattgcatatccgcccgtcc Mask Tandem Repeat Region ================================================ ggacgggcggatatgcaatgagacaatcaagcaattaagttacgagagcacttatcgagaagaaggacttgccgatttctcgatgagtgctctttctttttccacccaagcaaattg Find is-nt database================================================ Query_seq: PG0669:PG0670|PG0669:PG0670:heme-binding protein FetB:lipoprotein, putative:->->:720775..720891 117 ggacgggcggatatgcaatgagacaatcaagcaattaagttacgagagcacttatcgagaagaaggacttgccgatttctcgatgagtgctctttctttttccacccaagcaaattg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0669:PG0670|PG0669:PG0670:heme-binding protein FetB:lipoprotein, putative:->->:720775..720891 117 ggacgggcggatatgcaatgagacaatcaagcaattaagttacgagagcacttatcgagaagaaggacttgccgatttctcgatgagtgctctttctttttccacccaagcaaattg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0669:PG0670|PG0669:PG0670:heme-binding protein FetB:lipoprotein, putative:->->:720775..720891 117 ggacgggcggatatgcaatgagacaatcaagcaattaagttacgagagcacttatcgagaagaaggacttgccgatttctcgatgagtgctctttctttttccacccaagcaaattg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggacgggcggatatgcaatgagacaatcaagcaattaagttacgagagcacttatcgagaagaaggacttgccgatttctcgatgagtgctctttctttttccacccaagcaaattg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 11 End: 115 .......... M C N E T I K Q L S Y E S T Y R E E G L A D F S M S A L S F S T Q A N .. ggacgggcggatatgcaatgagacaatcaagcaattaagttacgagagcacttatcgagaagaaggacttgccgatttctcgatgagtgctctttctttttccacccaagcaaattg 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================================================ ggacgggcggatatgcaatgagacaatcaagcaattaagttacgagagcacttatcgagaagaaggacttgccgatttctcgatgagtgctctttctttttccacccaagcaaattg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.3 Tail_Score: -4.85782 Start: 46 End: 92 Full_Region: GCAATTAAGTTACGA GAGCACTTATCGAGAAGAAGG ACTTG CCGATTTCTCGATGAGTGCTC TTTCTTTTTCCACCC .............................................GAGCACTTATCGAGAAGAAGGACTTGCCGATTTCTCGATGAGTGCTC......................... TransTerm Strand: - Conf: 59 HP_score: -7.7 Tail_Score: -2.83677 Start: 48 End: 90 Full_Region: gtggaaaaagaaaga gcactcatcgagaaatcgg caagt ccttcttctcgataagtgc tctcgtaacttaatt ...............................................gcactcatcgagaaatcggcaagtccttcttctcgataagtgc........................... Find igs database================================================ Query_seq: PG0669:PG0670|PG0669:PG0670:heme-binding protein FetB:lipoprotein, putative:->->:720775..720891 117 ggacgggcggatatgcaatgagacaatcaagcaattaagttacgagagcacttatcgagaagaaggacttgccgatttctcgatgagtgctctttctttttccacccaagcaaattg Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_002950_PG0669_PG0670|heme-binding protein FetB:lipoprotein, putative|POSITIVE:POSITIVE|[720775,720891]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 ggacgggcggatatgcaatgagacaatcaagcaattaagttacgagagcacttatcgagaagaaggacttgccgatttctcgatgagtgctctttctttttccacccaagcaaattg ggacgggcggatatgcaatgagacaatcaagcaattaagttacgagagcacttatcgagaagaaggacttgccgatttctcgatgagtgctctttctttttccacccaagcaaattg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGACGGGCGGAUAUGCAAUGAGACAAUCAAGCAAUUAAGUUACGAGAGCACUUAUCGAGAAGAAGGACUUGCCGAUUUCUCGAUGAGUGCUCUUUCUUUUUCCACCCAAGCAAAUUG ....(((.(((..(((..(((.....))).)))..........(((((((((((((((((((..((.....))..)))))))))))))))))))......))).))).......... (-45.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUUUGCUUGGGUGGAAAAAGAAAGAGCACUCAUCGAGAAAUCGGCAAGUCCUUCUUCUCGAUAAGUGCUCUCGUAACUUAAUUGCUUGAUUGUCUCAUUGCAUAUCCGCCCGUCC ..........(((((((.......((((((((.((((((((...((.....))...)))))))).))))))))...........(((.(((.....)))..)))..))))))).... (-40.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 443 90 41 227 174 NC_002950:PG0889|5end_peptidase,_M24_family_950100..950330_POSITIVE 375 100 61 44 10 NC_002950:PG0888|5end_hypothetical_protein_949910..950140_POSITIVE 358 96 54 197 150 NC_002950:PG2003|5end_deoxyguanosinetriphosphate_triphosphohydrolase_2092991..2093221_NEGATIVE 346 90 46 223 170 NC_002950:PG1565|5end_3-deoxy-D-manno-octulosonic-acid_transferase,_putative_1645859..1646089_NEGATIVE 328 50 5 74 25 NC_002950:PG0613|5end_hypothetical_protein_665186..665416_POSITIVE 322 99 57 172 113 NC_002950:PG1978|5end_hypothetical_protein_2067337..2067567_NEGATIVE 318 49 4 208 156 NC_002950:PG0280|5end_ABC_transporter,_permease_protein,_putative_314625..314855_NEGATIVE 308 89 51 51 17 NC_002950:PG2086|5end_hypothetical_protein_2186571..2186801_POSITIVE 308 90 44 213 164 NC_002950:PG0127|5end_ferrochelatase_148550..148780_POSITIVE 302 100 56 99 46 NC_002950:PG1288|5end_GDP-mannose_4,6-dehydratase_1365963..1366193_POSITIVE 296 110 65 192 147 NC_002950:PG1449|5end_hypothetical_protein_1534262..1534492_NEGATIVE 296 110 65 192 147 NC_002950:PG0824|5end_hypothetical_protein_881170..881400_POSITIVE 294 96 57 140 96 NC_002950:PG2076|5end_hypothetical_protein_2176445..2176675_POSITIVE 294 96 57 140 96 NC_002950:PG1267|5end_hypothetical_protein_1346966..1347196_POSITIVE 291 104 66 84 39 NC_002950:PG1758|5end_ribosomal_protein_S15_1845185..1845415_POSITIVE 290 73 39 180 133 NC_002950:PG2089|5end_hypothetical_protein_2188640..2188870_POSITIVE 290 74 31 229 185 NC_002950:PG0772|5end_hypothetical_protein_824975..825205_POSITIVE 289 87 51 229 180 NC_002950:PG1324|5end_Holliday_junction_resolvase_1403431..1403661_NEGATIVE 289 89 56 131 93 NC_002950:PG1021|5end_hypothetical_protein_1083592..1083822_NEGATIVE 289 90 42 60 7 NC_002950:PG0307|5end_NADH-ubiquinone_oxidoreductase_342560..342790_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 90 48 43 1 NC_002950:PG0669|3end_heme-binding_protein_FetB_720714..720864_POSITIVE 358 96 54 53 6 NC_002950:PG2004|3end_hypothetical_protein_2093135..2093285_NEGATIVE 328 50 5 50 1 NC_002950:PG0612|3end_hypothetical_protein_665242..665392_POSITIVE 319 90 44 123 74 NC_002950:PG1758|3end_ribosomal_protein_S15_1845534..1845684_POSITIVE 304 106 63 70 17 NC_002950:PG0349|3end_hydrolase,_haloacid_dehalogenase-like_family_385291..385441_POSITIVE 290 73 39 123 76 NC_002950:PG2088|3end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_2188663..2188813_POSITIVE 290 100 51 138 83 NC_002950:PG1814|3end_DNA_primase_1908606..1908756_NEGATIVE 289 90 42 63 10 NC_002950:PG0306|3end_electron_transport_complex,_RnfABCDGE_type,_G_subunit_342643..342793_POSITIVE 287 90 43 42 1 NC_002950:PG0376|3end_30S_ribosomal_protein_S9_406865..407015_POSITIVE 286 90 44 133 85 NC_002950:PG0734|3end_nitroreductase_family_protein_784404..784554_POSITIVE 283 102 61 63 19 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE 279 59 23 102 61 NC_002950:PG0692|3end_4-hydroxybutyryl-CoA_dehydratase_747542..747692_NEGATIVE 279 94 55 69 28 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 278 98 54 73 21 NC_002950:PG1495|3end_DNA_topoisomerase_III_1573416..1573566_POSITIVE 278 89 44 148 101 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 277 100 51 98 38 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 274 108 61 87 47 NC_002950:PG0872|3end_mobilizable_transposon,_xis_protein_934846..934996_NEGATIVE 273 90 43 67 21 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 273 96 57 42 1 NC_002950:PG0195|3end_rubrerythrin_232704..232854_POSITIVE 270 49 4 132 73 NC_002950:PG1834|3end_glycogen_synthase-related_protein_1927050..1927200_POSITIVE