Origin IGS: aggtgatttttatgacagaaaaagaaattgaattatctatggataaggctttaaaaaaacttccttttgaaattaaaaaaataaaatttgttttagcagtgataaagttttttaaaaggaaataagaatatgattaattattgagctattgtaaaaataaatttgcaatagctttttatttttgatttaatataaaaaataagaaaaactttggagggaaatatgttagaagaaaaattgttaaagaaaataaaaaccatcaatgaaaattttataaat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttataaaattttcattgatggtttttattttctttaacaatttttcttctaacatatttccctccaaagtttttcttattttttatattaaatcaaaaataaaaagctattgcaaatttatttttacaatagctcaataattaatcatattcttatttccttttaaaaaactttatcactgctaaaacaaattttatttttttaatttcaaaaggaagtttttttaaagccttatccatagataattcaatttctttttctgtcataaaaatcacct Mask Tandem Repeat Region ================================================ aggtgatttttatgacagaaaaagaaattgaattatctatggataaggctttaaaaaaacttccttttgaaattaaaaaaataaaatttgttttagcagtgataaagttttttaaaaggaaataagaatatgattaattattgagctattgtaaaaataaatttgcaatagctttttatttttgatttaatataaaaaataagaaaaactttggagggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaaaaaccatcaatgaaaattttataaat Find is-nt database================================================ Query_seq: FN0164:FN0165|FN0164:FN0165:Anhydro-N-acetylmuramyl-tripeptide amidase:hypothetical protein:->->:793352..793630 279 aggtgatttttatgacagaaaaagaaattgaattatctatggataaggctttaaaaaaacttccttttgaaattaaaaaaataaaatttgttttagcagtgataaagttttttaaaaggaaataagaatatgattaattattgagctattgtaaaaataaatttgcaatagctttttatttttgatttaatataaaaaataagaaaaactttggagggaaatatgttagaagaaaaattgttaaagaaaataaaaaccatcaatgaaaattttataaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0164:FN0165|FN0164:FN0165:Anhydro-N-acetylmuramyl-tripeptide amidase:hypothetical protein:->->:793352..793630 279 aggtgatttttatgacagaaaaagaaattgaattatctatggataaggctttaaaaaaacttccttttgaaattaaaaaaataaaatttgttttagcagtgataaagttttttaaaaggaaataagaatatgattaattattgagctattgtaaaaataaatttgcaatagctttttatttttgatttaatataaaaaataagaaaaactttggagggaaatatgttagaagaaaaattgttaaagaaaataaaaaccatcaatgaaaattttataaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0164:FN0165|FN0164:FN0165:Anhydro-N-acetylmuramyl-tripeptide amidase:hypothetical protein:->->:793352..793630 279 aggtgatttttatgacagaaaaagaaattgaattatctatggataaggctttaaaaaaacttccttttgaaattaaaaaaataaaatttgttttagcagtgataaagttttttaaaaggaaataagaatatgattaattattgagctattgtaaaaataaatttgcaatagctttttatttttgatttaatataaaaaataagaaaaactttggagggaaatatgttagaagaaaaattgttaaagaaaataaaaaccatcaatgaaaattttataaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggtgatttttatgacagaaaaagaaattgaattatctatggataaggctttaaaaaaacttccttttgaaattaaaaaaataaaatttgttttagcagtgataaagttttttaaaaggaaataagaatatgattaattattgagctattgtaaaaataaatttgcaatagctttttatttttgatttaatataaaaaataagaaaaactttggagggaaatatgttagaagaaaaattgttaaagaaaataaaaaccatcaatgaaaattttataaat Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 3 End: 122 .. M I F M T E K E I E L S M D K A L K K L P F E I K K I K F V L A V I K F F K R K ............................................................................................................................................................. Protein_Len: 45 Strand: - Start: 141 End: 275 ............................................................................................................................................ Q A I T F I F K C Y S K I K S K I Y F I L F V K S P F I N S S F N N F F I F V M L S F K M .... Protein_Len: 34 Strand: - Start: 2 End: 103 . T I K I V S F S I S N D I S L A K F F S G K S I L F I F N T K A T M ................................................................................................................................................................................ aggtgatttttatgacagaaaaagaaattgaattatctatggataaggctttaaaaaaacttccttttgaaattaaaaaaataaaatttgttttagcagtgataaagttttttaaaaggaaataagaatatgattaattattgagctattgtaaaaataaatttgcaatagctttttatttttgatttaatataaaaaataagaaaaactttggagggaaatatgttagaagaaaaattgttaaagaaaataaaaaccatcaatgaaaattttataaat 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: 82 Start: 162 End: 191 .................................................................................................................................................................TTTGCAATAGCTTTTTATTTTTGATTTAAT........................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggtgatttttatgacagaaaaagaaattgaattatctatggataaggctttaaaaaaacttccttttgaaattaaaaaaataaaatttgttttagcagtgataaagttttttaaaaggaaataagaatatgattaattattgagctattgtaaaaataaatttgcaatagctttttatttttgatttaatataaaaaataagaaaaactttggagggaaatatgttagaagaaaaattgttaaagaaaataaaaaccatcaatgaaaattttataaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -2.5 Tail_Score: -5.72207 Start: 82 End: 95 Full_Region: aaactttatcactgc taaaa caaa tttta tttttttaatttcaa .................................................................................taaaacaaatttta........................................................................................................................................................................................ TransTerm Strand: + Conf: 95 HP_score: -7.9 Tail_Score: -5.67529 Start: 145 End: 172 Full_Region: ATGATTAATTATTGA GCTATTGTAAA AATAAA TTTGCAATAGC TTTTTATTTTTGATT ................................................................................................................................................GCTATTGTAAAAATAAATTTGCAATAGC........................................................................................................... Find igs database================================================ Query_seq: FN0164:FN0165|FN0164:FN0165:Anhydro-N-acetylmuramyl-tripeptide amidase:hypothetical protein:->->:793352..793630 279 aggtgatttttatgacagaaaaagaaattgaattatctatggataaggctttaaaaaaacttccttttgaaattaaaaaaataaaatttgttttagcagtgataaagttttttaaaaggaaataagaatatgattaattattgagctattgtaaaaataaatttgcaatagctttttatttttgatttaatataaaaaataagaaaaactttggagggaaatatgttagaagaaaaattgttaaagaaaataaaaaccatcaatgaaaattttataaat Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: NC_003454_FN0164_FN0165|Anhydro-N-acetylmuramyl-tripeptide amidase:hypothetical protein|POSITIVE:POSITIVE|[793352,793630]|279 HSP 1 e-value: 3.0E-21 bit: 103.0 Len: 52 Query Start:1 Query End:52 Subject Strand: POSITIVE Subject Start: 1 Subject End: 52 aggtgatttttatgacagaaaaagaaattgaattatctatggataaggcttt................................................................................................................................................................................................................................... aggtgatttttatgacagaaaaagaaattgaattatctatggataaggcttt................................................................................................................................................................................................................................... HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 34 Query Start:118 Query End:151 Subject Strand: POSITIVE Subject Start: 118 Subject End: 151 .....................................................................................................................ggaaataagaatatgattaattattgagctattg................................................................................................................................ .....................................................................................................................ggaaataagaatatgattaattattgagctattg................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUGAUUUUUAUGACAGAAAAAGAAAUUGAAUUAUCUAUGGAUAAGGCUUUAAAAAAACUUCCUUUUGAAAUUAAAAAAAUAAAAUUUGUUUUAGCAGUGAUAAAGUUUUUUAAAAGGAAAUAAGAAUAUGAUUAAUUAUUGAGCUAUUG .(((((((.(((((...............(..(((((....)))))..)...........((((((((((((..............((((((........))))))...)))))))))))).......)))))..)))))))......... (-18.93) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUAGCUCAAUAAUUAAUCAUAUUCUUAUUUCCUUUUAAAAAACUUUAUCACUGCUAAAACAAAUUUUAUUUUUUUAAUUUCAAAAGGAAGUUUUUUUAAAGCCUUAUCCAUAGAUAAUUCAAUUUCUUUUUCUGUCAUAAAAAUCACCU ..((((...........................((((.((((((((((........(((((.((......)).)))))..........)))))))))).))))..(((((....)))))..............)))).............. ( -9.07) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 232 123 81 182 139 NC_003454:FN0582|5end_Lipoprotein_releasing_system_ATP-binding_protein_lolD_1238246..1238476_POSITIVE 227 74 41 60 24 NC_003454:FN1995|5end_hypothetical_protein_498245..498475_POSITIVE 188 68 23 119 78 NC_003454:FN1414|5end_NA+/H+_antiporter_NHAC_2075559..2075789_NEGATIVE 187 78 36 117 69 NC_003454:FN1049|5end_hypothetical_protein_1699035..1699265_POSITIVE 184 91 54 169 134 NC_003454:FN0121|5end_hypothetical_protein_753300..753530_NEGATIVE 183 120 80 152 115 NC_003454:FN1034|5end_Transcriptional_regulator,_TetR_family_1687648..1687878_POSITIVE 181 121 88 39 1 NC_003454:FN1474|5end_N-acetylmannosamine_kinase_2156888..2157118_POSITIVE 177 53 23 107 68 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 174 65 28 80 37 NC_003454:FN0419|5end_aspartate_carbamoyltransferase_catalytic_subunit_1059713..1059943_POSITIVE 172 109 61 153 101 NC_003454:FN0684|5end_hydroxylamine_reductase_1338891..1339121_POSITIVE 170 69 32 66 20 NC_003454:FN0728|5end_hypothetical_protein_1386120..1386350_NEGATIVE 170 49 7 122 85 NC_003454:FN1985|5end_Inner_membrane_protein_488637..488867_NEGATIVE 166 130 84 49 3 NC_003454:FN0928|5end_O-sialoglycoprotein_endopeptidase_1583026..1583256_NEGATIVE 163 130 89 166 125 NC_003454:FN0998|5end_Dipeptide-binding_protein_1652247..1652477_POSITIVE 163 81 44 86 49 NC_003454:FN0828|5end_ABC_transporter_permease_protein_1488199..1488429_POSITIVE 163 50 2 112 65 NC_003454:FN0102|5end_Ribonucleoside-diphosphate_reductase_alpha_chain_736233..736463_POSITIVE 161 71 37 77 40 NC_003454:FN1468|5end_Flavoredoxin_2150385..2150615_NEGATIVE 160 128 82 184 140 NC_003454:FN1783|5end_Ethanolamine_utilization_protein_eutJ_264626..264856_POSITIVE 157 112 81 62 30 NC_003454:FN1008|5end_hypothetical_protein_1663067..1663297_NEGATIVE 155 68 22 106 56 NC_003454:FN1403|5end_Histidine_permease_2061743..2061973_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 191 110 72 119 78 NC_003454:FN0178|3end_UNC-44_ankyrins_802390..802540_NEGATIVE 188 68 23 70 29 NC_003454:FN1415|3end_NADH-dependent_butanol_dehydrogenase_A_2075608..2075758_NEGATIVE 187 78 36 96 48 NC_003454:FN1048|3end_Hypothetical_membrane-spanning_protein_1699094..1699244_POSITIVE 179 150 102 95 34 NC_003454:FN1732|3end_hypothetical_protein_231281..231431_NEGATIVE 166 130 84 68 22 NC_003454:FN0929|3end_ATP/GTP_hydrolase_1583007..1583157_NEGATIVE 163 81 44 89 52 NC_003454:FN0827|3end_ABC_transporter_ATP-binding_protein_1488282..1488432_POSITIVE 163 50 2 112 65 NC_003454:FN0101|3end_Glutaredoxin_736313..736463_POSITIVE 161 71 37 75 38 NC_003454:FN1469|3end_Na+_driven_multidrug_efflux_pump_2150387..2150537_NEGATIVE 154 50 25 62 35 NC_003454:FN0160|3end_hypothetical_protein_788598..788748_POSITIVE 154 102 63 141 102 NC_003454:FN1844|3end_Ketoacyl_reductase_hetN_334446..334596_POSITIVE 153 68 39 68 40 NC_003454:FN2064|3end_hypothetical_protein_575213..575363_NEGATIVE 152 70 32 150 109 NC_003454:FN0656|3end_hypothetical_protein_1314185..1314335_POSITIVE 151 65 27 84 46 NC_003454:FN0493|3end_hypothetical_protein_1137623..1137773_NEGATIVE 150 67 32 42 12 NC_003454:FN0271|3end_Enoyl-CoA_hydratase_898721..898871_POSITIVE 150 137 95 79 35 NC_003454:FN2087|3end_hypothetical_protein_599039..599189_NEGATIVE 150 89 60 68 39 NC_003454:FN1803|3end_Transcriptional_regulator,_TetR_family_284947..285097_POSITIVE 148 121 91 36 1 NC_003454:FN1473|3end_N-acetylneuraminate_transporter_large_subunit_2156965..2157115_POSITIVE 148 89 41 92 52 NC_003454:FN1656|3end_SSU_ribosomal_protein_S18P_152542..152692_NEGATIVE 147 50 2 70 21 NC_003454:FN1987|3end_Transcriptional_regulator,_GntR_family_490018..490168_NEGATIVE 146 114 82 139 109 NC_003454:FN1462|3end_Transcriptional_regulator,_GntR_family_2143536..2143686_NEGATIVE