Origin IGS: tattatttcctcctattctttatctcaagttaattttcctgtttcaactgcaacttcatatcttgcaatcttataatttaatttttccaaagtttcctctatctgttttctttgtttcaacaatttttctctctgttcctttaaaagatcacattttgcttgaattgttgaagttcttctttctaaacaattttattttaccattttaacttagctctaagtcaagagaaatttttaaatattttatattttttattttttcttgatttttcaacataaaatattataataaatatagaagttataattggaaatagaaaagagggaatt .........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 aattccctcttttctatttccaattataacttctatatttattataatattttatgttgaaaaatcaagaaaaaataaaaaatataaaatatttaaaaatttctcttgacttagagctaagttaaaatggtaaaataaaattgtttagaaagaagaacttcaacaattcaagcaaaatgtgatcttttaaaggaacagagagaaaaattgttgaaacaaagaaaacagatagaggaaactttggaaaaattaaattataagattgcaagatatgaagttgcagttgaaacaggaaaattaacttgagataaagaataggaggaaataata Mask Tandem Repeat Region ================================================ tattatttcctcctattctttatctcaagttaattttcctgtttcaactgcaacttcatatcttgcaatcttataatttaatttttccaaagtttcctctatctgttttctttgtttcaacaatttttctctctgttcctttaaaagatcacattttgcttgaattgttgaagttcttctttctaaacaattttattttaccattttaacttagctctaagtcaagagaaatttttaaatattttatattttttattttttcttgatttttcaacataaaatattataataaatatagaagttataattggaaatagaaaagagggaatt Find is-nt database================================================ Query_seq: FN1464:FN1465|FN1464:FN1465:1-deoxy-D-xylulose-5-phosphate synthase:Permease:<-->:2147796..2148125 330 tattatttcctcctattctttatctcaagttaattttcctgtttcaactgcaacttcatatcttgcaatcttataatttaatttttccaaagtttcctctatctgttttctttgtttcaacaatttttctctctgttcctttaaaagatcacattttgcttgaattgttgaagttcttctttctaaacaattttattttaccattttaacttagctctaagtcaagagaaatttttaaatattttatattttttattttttcttgatttttcaacataaaatattataataaatatagaagttataattggaaatagaaaagagggaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1464:FN1465|FN1464:FN1465:1-deoxy-D-xylulose-5-phosphate synthase:Permease:<-->:2147796..2148125 330 tattatttcctcctattctttatctcaagttaattttcctgtttcaactgcaacttcatatcttgcaatcttataatttaatttttccaaagtttcctctatctgttttctttgtttcaacaatttttctctctgttcctttaaaagatcacattttgcttgaattgttgaagttcttctttctaaacaattttattttaccattttaacttagctctaagtcaagagaaatttttaaatattttatattttttattttttcttgatttttcaacataaaatattataataaatatagaagttataattggaaatagaaaagagggaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1464:FN1465|FN1464:FN1465:1-deoxy-D-xylulose-5-phosphate synthase:Permease:<-->:2147796..2148125 330 tattatttcctcctattctttatctcaagttaattttcctgtttcaactgcaacttcatatcttgcaatcttataatttaatttttccaaagtttcctctatctgttttctttgtttcaacaatttttctctctgttcctttaaaagatcacattttgcttgaattgttgaagttcttctttctaaacaattttattttaccattttaacttagctctaagtcaagagaaatttttaaatattttatattttttattttttcttgatttttcaacataaaatattataataaatatagaagttataattggaaatagaaaagagggaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 16 Max: 192 Len: 177 Subject: UniRef90_Q7P482 Cluster: Transcriptional regulator, MerR family; n=1; Fusobacterium nucleatum subsp. vincentii ATCC 49256|Rep: Transcriptional regulator, MerR family - Fusobacterium nucleatum subsp. vincentii ATCC 49256 HSP 1 e-value: 1.0E-8 bit: 60.8 Len: 177 Query Start:16 Query End:192 Subject Strand: null Subject Start: 68 Subject End: 126 ............... N C L E R R T S T I Q A K C D X X X X X X X X X X X X X X Q I E E T L E K L N Y K I A R Y E V A V E T G K L T * D K E .......................................................................................................................................... ............... N L Y K Q G D S T I Q A R C N L L Q E Q R D K L L E Q R K Q I E E T L E N L H Y K I A R Y E V A V E T G K L T W D K E .......................................................................................................................................... tattatttcctcctannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttattttaccattttaacttagctctaagtcaagagaaatttttaaatattttatattttttattttttcttgatttttcaacataaaatattataataaatatagaagttataattggaaatagaaaagagggaatt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 15 End: 206 .............. M L Y L K L I F L F Q L Q L H I L Q S Y N L I F P K F P L S V F F V S T I F L S V P L K D H I L L E L L K F F F L N N F ............................................................................................................................ Protein_Len: 35 Strand: - Start: 225 End: 329 ................................................................................................................................................................................................................................ S F N K F I K Y K K N K R S K E V Y F I I I F I S T I I P F L F S P M . Protein_Len: 46 Strand: - Start: 28 End: 165 ........................... T L K G T E V A V E Y R A I K Y N L K E L T E E I Q K R Q K L L K E R Q E K L L D C K A Q M ..................................................................................................................................................................... tattatttcctcctannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttattttaccattttaacttagctctaagtcaagagaaatttttaaatattttatattttttattttttcttgatttttcaacataaaatattataataaatatagaagttataattggaaatagaaaagagggaatt 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: 286 End: 315 .............................................................................................................................................................................................................................................................................................ATTTCCAATTATAACTTCTATATTTATTAT............... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattatttcctcctannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttattttaccattttaacttagctctaagtcaagagaaatttttaaatattttatattttttattttttcttgatttttcaacataaaatattataataaatatagaagttataattggaaatagaaaagagggaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1464:FN1465|FN1464:FN1465:1-deoxy-D-xylulose-5-phosphate synthase:Permease:<-->:2147796..2148125 330 tattatttcctcctannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttattttaccattttaacttagctctaagtcaagagaaatttttaaatattttatattttttattttttcttgatttttcaacataaaatattataataaatatagaagttataattggaaatagaaaagagggaatt Intra-Species Hit: Count: 1 Min: 193 Max: 330 Len: 138 Subject: NC_003454_FN1464_FN1465|1-deoxy-D-xylulose-5-phosphate synthase:Permease|NEGATIVE:POSITIVE|[2147796, 2148125]|330 HSP 1 e-value: 3.0E-25 bit: 117.0 Len: 59 Query Start:272 Query End:330 Subject Strand: POSITIVE Subject Start: 272 Subject End: 330 ...............................................................................................................................................................................................................................................................................caacataaaatattataataaatatagaagttataattggaaatagaaaagagggaatt ...............................................................................................................................................................................................................................................................................caacataaaatattataataaatatagaagttataattggaaatagaaaagagggaatt HSP 2 e-value: 9.0E-13 bit: 75.8 Len: 38 Query Start:193 Query End:230 Subject Strand: POSITIVE Subject Start: 193 Subject End: 230 ................................................................................................................................................................................................ttattttaccattttaacttagctctaagtcaagagaa.................................................................................................... ................................................................................................................................................................................................ttattttaccattttaacttagctctaagtcaagagaa.................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUUUACCAUUUUAACUUAGCUCUAAGUCAAGAGAAAUUUUUAAAUAUUUUAUAUUUUUUAUUUUUUCUUGAUUUUUCAACAUAAAAUAUUAUAAUAAAUAUAGAAGUUAUAAUUGGAAAUAGAAAAGAGGGAAUU ((((((..(((...((((((......(((((((((((((.....((((((...)))))).....)))))))))))))...........(((((......)))))..))))))....)))))))))............. (-20.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCCCUCUUUUCUAUUUCCAAUUAUAACUUCUAUAUUUAUUAUAAUAUUUUAUGUUGAAAAAUCAAGAAAAAAUAAAAAAUAUAAAAUAUUUAAAAAUUUCUCUUGACUUAGAGCUAAGUUAAAAUGGUAAAAUAA ..............((((((((...................(((.(((((((((((((......................)))))))))))))))).........((((((((....))))))))..)))..))))). (-15.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 201 80 39 44 2 NC_003454:FN0197|5end_Methyltransferase_822664..822894_POSITIVE 194 42 1 216 175 NC_003454:FN2124|5end_Hypothetical_protein_with_Metallo-phosphoesterase_motif_633712..633942_NEGATIVE 188 47 1 76 31 NC_003454:FN1375|5end_Citrate-sodium_symport_2022416..2022646_POSITIVE 187 130 100 226 190 NC_003454:FN1955|5end_hypothetical_protein_459936..460166_POSITIVE 186 80 40 138 101 NC_003454:FN0907|5end_Ribosomal_RNA_small_subunit_methyltransferase_C_1565995..1566225_NEGATIVE 186 78 32 107 58 NC_003454:FN0235|5end_ABC_transporter_ATP-binding_protein_860402..860632_NEGATIVE 184 70 23 52 10 NC_003454:FN1142|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1791529..1791759_POSITIVE 184 76 43 40 7 NC_003454:FN0829|5end_hypothetical_protein_1489873..1490103_NEGATIVE 183 78 47 117 83 NC_003454:FN1490|5end_4-hydroxybenzoate_octaprenyltransferase_2172283..2172513_NEGATIVE 183 118 77 87 34 NC_003454:FN0800|5end_Amino_acid-binding_protein_1460639..1460869_NEGATIVE 183 70 21 203 153 NC_003454:FN1747|5end_Cysteine_permease_245647..245877_POSITIVE 181 86 45 123 77 NC_003454:FN0684|5end_hydroxylamine_reductase_1338891..1339121_POSITIVE 179 80 53 58 29 NC_003454:FN1096|5end_hypothetical_protein_1740587..1740817_POSITIVE 179 67 21 190 148 NC_003454:FN0881|5end_ABC_transporter_integral_membrane_protein_1542747..1542977_NEGATIVE 178 31 1 50 15 NC_003454:FN0132|5end_Hemolysin_761715..761945_POSITIVE 177 127 81 87 37 NC_003454:FN0341|5end_transport_protein_975381..975611_NEGATIVE 176 46 1 133 94 NC_003454:FN1730|5end_Anthranilate_synthase_component_I_230442..230672_NEGATIVE 175 81 58 65 42 NC_003454:FN0890|5end_Thiamin_pyrophosphokinase_1552087..1552317_NEGATIVE 172 70 24 228 186 NC_003454:FN1341|5end_Bacterial_Peptide_Chain_Release_Factor_2_(RF-2)_1995896..1996126_NEGATIVE 172 100 65 36 1 NC_003454:FN1095|5end_hypothetical_protein_1740232..1740462_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 204 69 21 86 37 NC_003454:FN0322|3end_fructose-bisphosphate_aldolase_960580..960730_POSITIVE 201 80 39 47 5 NC_003454:FN0196|3end_Transcriptional_regulator,_FUR_family_822747..822897_POSITIVE 193 82 57 143 118 NC_003454:FN1119|3end_50S_ribosomal_protein_L27_1761253..1761403_POSITIVE 187 70 27 117 74 NC_003454:FN0803|3end_trifunctional_thioredoxin/methionine_sulfoxide_reductase_A/B_protein_1462450..1462600_NEGATIVE 186 80 40 136 99 NC_003454:FN0908|3end_Tpl_protein_1565997..1566147_NEGATIVE 186 78 32 97 48 NC_003454:FN0236|3end_ABC_transporter_substrate-binding_protein_860412..860562_NEGATIVE 183 78 47 98 64 NC_003454:FN1491|3end_PTS_system,_IIA_component_2172302..2172452_NEGATIVE 179 80 53 65 36 NC_003454:FN1095|3end_hypothetical_protein_1740674..1740824_POSITIVE 177 29 2 151 123 NC_003454:FN1795|3end_hypothetical_protein_275739..275889_NEGATIVE 176 72 32 118 77 NC_003454:FN0174|3end_Enoyl-[acyl-carrier-protein]_reductase_800463..800613_POSITIVE 176 46 1 149 110 NC_003454:FN1731|3end_Anthranilate_synthase_component_II_230426..230576_NEGATIVE 175 81 58 65 42 NC_003454:FN0891|3end_DNAse_I_homologous_protein_DHP2_precursor_1552087..1552237_NEGATIVE 169 86 41 117 65 NC_003454:FN1942|3end_Hypothetical_cytosolic_protein_444000..444150_NEGATIVE 168 66 24 96 53 NC_003454:FN1453|3end_hypothetical_protein_2134073..2134223_NEGATIVE 167 80 33 100 56 NC_003454:FN1650|3end_Oligopeptide_transport_system_permease_protein_oppC_144118..144268_NEGATIVE 161 32 1 139 104 NC_003454:FN0119|3end_Flavodoxin_752647..752797_POSITIVE 160 79 31 105 60 NC_003454:FN0656|3end_hypothetical_protein_1314185..1314335_POSITIVE 159 64 21 150 106 NC_003454:FN1746|3end_Cystathionine_beta-lyase_245680..245830_POSITIVE 158 90 41 70 24 NC_003454:FN0277|3end_hypothetical_protein_903421..903571_NEGATIVE 158 78 39 113 77 NC_003454:FN1908|3end_Glycerophosphoryl_diester_phosphodiesterase_400596..400746_NEGATIVE