Origin IGS: ggaaataaaattttactatatttgtactagtttcataatctttaagaaaattcataaagtttagtcaaaattcttttgatttttttgactaatttaaattgaggttatagtaaatttaataatctactacaacctcttattttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaaataagaggttgtagtagattattaaatttactataacctcaatttaaattagtcaaaaaaatcaaaagaattttgactaaactttatgaattttcttaaagattatgaaactagtacaaatatagtaaaattttatttcc Mask Tandem Repeat Region ================================================ ggaaataaaattttactatatttgtactagtttcataatctttaagaaaattcataaagtttagtcaaaattcttttgatttttttgactaatttaaattgaggttatagtaaatttaataatctactacaacctcttattttat Find is-nt database================================================ Query_seq: FN1108:FN1109|FN1108:FN1109:Phosphohydrolase (MUTT/NUDIX family protein):Dipeptide transport ATP-binding protein dppF:-><-:1752939..1753083 145 ggaaataaaattttactatatttgtactagtttcataatctttaagaaaattcataaagtttagtcaaaattcttttgatttttttgactaatttaaattgaggttatagtaaatttaataatctactacaacctcttattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1108:FN1109|FN1108:FN1109:Phosphohydrolase (MUTT/NUDIX family protein):Dipeptide transport ATP-binding protein dppF:-><-:1752939..1753083 145 ggaaataaaattttactatatttgtactagtttcataatctttaagaaaattcataaagtttagtcaaaattcttttgatttttttgactaatttaaattgaggttatagtaaatttaataatctactacaacctcttattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1108:FN1109|FN1108:FN1109:Phosphohydrolase (MUTT/NUDIX family protein):Dipeptide transport ATP-binding protein dppF:-><-:1752939..1753083 145 ggaaataaaattttactatatttgtactagtttcataatctttaagaaaattcataaagtttagtcaaaattcttttgatttttttgactaatttaaattgaggttatagtaaatttaataatctactacaacctcttattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggaaataaaattttactatatttgtactagtttcataatctttaagaaaattcataaagtttagtcaaaattcttttgatttttttgactaatttaaattgaggttatagtaaatttaataatctactacaacctcttattttat Predict ORF larger than 30AA ================================================ ggaaataaaattttactatatttgtactagtttcataatctttaagaaaattcataaagtttagtcaaaattcttttgatttttttgactaatttaaattgaggttatagtaaatttaataatctactacaacctcttattttat 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================================================ ggaaataaaattttactatatttgtactagtttcataatctttaagaaaattcataaagtttagtcaaaattcttttgatttttttgactaatttaaattgaggttatagtaaatttaataatctactacaacctcttattttat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -5.8 Tail_Score: -5.49729 Start: 65 End: 79 Full_Region: ATTCATAAAGTTTAG TCAAAA TTC TTTTGA TTTTTTTGACTAATT ................................................................TCAAAATTCTTTTGA.................................................................. Find igs database================================================ Query_seq: FN1108:FN1109|FN1108:FN1109:Phosphohydrolase (MUTT/NUDIX family protein):Dipeptide transport ATP-binding protein dppF:-><-:1752939..1753083 145 ggaaataaaattttactatatttgtactagtttcataatctttaagaaaattcataaagtttagtcaaaattcttttgatttttttgactaatttaaattgaggttatagtaaatttaataatctactacaacctcttattttat Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_003454_FN1108_FN1109|Phosphohydrolase (MUTT/NUDIX family protein):Dipeptide transport ATP-binding protein dppF|POSITIVE:NEGATIVE|[1752939,1753083]|145 HSP 1 e-value: 2.0E-64 bit: 246.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 ggaaataaaattttactatatttgtactagtttcataatctttaagaaaattcataaagtttagtcaaaattcttttgannnnnnngactaatttaaattgaggttatagtaaatttaataatctactacaacctcttattttat ggaaataaaattttactatatttgtactagtttcataatctttaagaaaattcataaagtttagtcaaaattcttttgatttttttgactaatttaaattgaggttatagtaaatttaataatctactacaacctcttattttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAAUAAAAUUUUACUAUAUUUGUACUAGUUUCAUAAUCUUUAAGAAAAUUCAUAAAGUUUAGUCAAAAUUCUUUUGAUUUUUUUGACUAAUUUAAAUUGAGGUUAUAGUAAAUUUAAUAAUCUACUACAACCUCUUAUUUUAU .((((((................................(((((.((....)).))))).((((((((((.((....))...))))))))))........((((((.(((((.(((....))).))))).)))))).)))))).. (-26.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAUAAGAGGUUGUAGUAGAUUAUUAAAUUUACUAUAACCUCAAUUUAAAUUAGUCAAAAAAAUCAAAAGAAUUUUGACUAAACUUUAUGAAUUUUCUUAAAGAUUAUGAAACUAGUACAAAUAUAGUAAAAUUUUAUUUCC (((((((..((((((((((((((((....))))))))))))))))........((((((((((...((....)).)))))))))).(((((.((....)).)))))........((((.........))))...))))))).... (-33.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 118 71 78 28 NC_003454:FN1563|5end_hypothetical_protein_85040..85270_NEGATIVE 210 43 7 86 49 NC_003454:FN1696|5end_UDP-4-dehydro-6-deoxy-2-acetamido-D-glucose_4-reductase_192699..192929_NEGATIVE 200 73 33 146 106 NC_003454:FN0266|5end_membrane_protein_related_to_metalloendopeptidase_892320..892550_POSITIVE 198 80 31 50 2 NC_003454:FN0338|5end_hypothetical_protein_971673..971903_POSITIVE 197 97 51 123 87 NC_003454:FN1401|5end_urocanate_hydratase_2058592..2058822_POSITIVE 194 99 51 191 147 NC_003454:FN1634|5end_LSU_ribosomal_protein_L24P_136179..136409_NEGATIVE 186 88 42 112 63 NC_003454:FN0670|5end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1325702..1325932_POSITIVE 182 99 51 230 175 NC_003454:FN2120|5end_Hypothetical_exported_24-amino_acid_repeat_protein_628930..629160_NEGATIVE 180 78 32 48 2 NC_003454:FN0382|5end_hypothetical_protein_1013257..1013487_POSITIVE 178 83 41 117 74 NC_003454:FN0782|5end_Methyltransferase_1439012..1439242_NEGATIVE 178 136 99 182 153 NC_003454:FN2038|5end_LSU_ribosomal_protein_L10P_547696..547926_NEGATIVE 177 112 76 53 14 NC_003454:FN0927|5end_hypothetical_protein_1582352..1582582_NEGATIVE 177 64 21 73 35 NC_003454:FN0439|5end_hypothetical_protein_1081610..1081840_NEGATIVE 173 48 18 38 5 NC_003454:FN1372|5end_Ribosomal_large_subunit_pseudouridine_synthase_D_2020981..2021211_NEGATIVE 170 110 61 197 149 NC_003454:FN1298|5end_Adenylate_kinase_1955626..1955856_NEGATIVE 170 136 100 180 146 NC_003454:FN0822|5end_Shikimate_kinase_1481828..1482058_POSITIVE 168 113 73 128 73 NC_003454:FN1516|5end_hypothetical_protein_20858..21088_NEGATIVE 167 86 42 111 57 NC_003454:FN0997|5end_hypothetical_protein_1652034..1652264_NEGATIVE 167 54 21 114 71 NC_003454:FN1623|5end_Ribosome_Recycling_Factor_(RRF)_130394..130624_POSITIVE 165 114 71 71 23 NC_003454:FN0829|5end_hypothetical_protein_1489873..1490103_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 210 43 7 86 49 NC_003454:FN1697|3end_hypothetical_protein_192699..192849_NEGATIVE 182 99 51 124 69 NC_003454:FN2121|3end_Hypothetical_exported_24-amino_acid_repeat_protein_629036..629186_NEGATIVE 170 110 61 128 80 NC_003454:FN1299|3end_dTDP-glucose_4,6-dehydratase_1955695..1955845_NEGATIVE 170 136 100 77 43 NC_003454:FN0821|3end_hypothetical_protein_1481805..1481955_POSITIVE 170 111 71 53 12 NC_003454:FN1918|3end_SPO0B-associated_GTP-binding_protein_413740..413890_NEGATIVE 168 67 33 148 116 NC_003454:FN0265|3end_Cell_division_protein_ftsX_892410..892560_POSITIVE 168 92 51 105 58 NC_003454:FN1954|3end_Glycerophosphoryl_diester_phosphodiesterase_459777..459927_NEGATIVE 168 113 73 110 55 NC_003454:FN1517|3end_Leucyl-tRNA_synthetase_20876..21026_NEGATIVE 167 54 21 79 36 NC_003454:FN1622|3end_Uridylate_kinase_130439..130589_POSITIVE 163 140 96 94 39 NC_003454:FN1975|3end_ATP-dependent_RNA_helicase_477265..477415_POSITIVE 160 49 8 105 63 NC_003454:FN0663|3end_hypothetical_protein_1319797..1319947_POSITIVE 158 45 15 101 69 NC_003454:FN0716|3end_Phophatidylinositol-4-phosphate_5-kinase_1374993..1375143_POSITIVE 157 100 57 107 65 NC_003454:FN1075|3end_hypothetical_protein_1722769..1722919_POSITIVE 157 84 52 134 107 NC_003454:FN1611|3end_Competence_protein_120597..120747_NEGATIVE 154 55 16 76 44 NC_003454:FN0655|3end_hypothetical_protein_1313790..1313940_POSITIVE 153 43 6 45 11 NC_003454:FN0868|3end_ATPase_of_the_PP_superfamily_1527217..1527367_NEGATIVE 153 60 12 106 60 NC_003454:FN0581|3end_Lipoprotein_releasing_system_transmembrane_protein_lolE_1238357..1238507_POSITIVE 152 43 8 88 56 NC_003454:FN0576|3end_D-amino_acid_dehydrogenase_large_subunit_1227302..1227452_POSITIVE 152 136 101 28 1 NC_003454:FN2039|3end_50S_ribosomal_protein_L1_547850..548000_NEGATIVE 152 86 43 151 115 NC_003454:FN1635|3end_LSU_ribosomal_protein_L14P_136204..136354_NEGATIVE