Origin IGS: caaatgtattaaatattataaggtaaagtcttattgaaaatgttgagatttaatgataaaataatagaaatatggtaatttaagattggggaggtaaataaagaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttctttatttacctccccaatcttaaattaccatatttctattattttatcattaaatctcaacattttcaataagactttaccttataatatttaatacatttg Mask Tandem Repeat Region ================================================ caaatgtattaaatattataaggtaaagtcttattgaaaatgttgagatttaatgataaaataatagaaatatggtaatttaagattggggaggtaaataaagaa Find is-nt database================================================ Query_seq: FN1796:FN1797|FN1796:FN1797:hypothetical protein:Spermidine/putrescine transport ATP-binding protein potA:->->:278856..278960 105 caaatgtattaaatattataaggtaaagtcttattgaaaatgttgagatttaatgataaaataatagaaatatggtaatttaagattggggaggtaaataaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1796:FN1797|FN1796:FN1797:hypothetical protein:Spermidine/putrescine transport ATP-binding protein potA:->->:278856..278960 105 caaatgtattaaatattataaggtaaagtcttattgaaaatgttgagatttaatgataaaataatagaaatatggtaatttaagattggggaggtaaataaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1796:FN1797|FN1796:FN1797:hypothetical protein:Spermidine/putrescine transport ATP-binding protein potA:->->:278856..278960 105 caaatgtattaaatattataaggtaaagtcttattgaaaatgttgagatttaatgataaaataatagaaatatggtaatttaagattggggaggtaaataaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaatgtattaaatattataaggtaaagtcttattgaaaatgttgagatttaatgataaaataatagaaatatggtaatttaagattggggaggtaaataaagaa Predict ORF larger than 30AA ================================================ caaatgtattaaatattataaggtaaagtcttattgaaaatgttgagatttaatgataaaataatagaaatatggtaatttaagattggggaggtaaataaagaa 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: 88 Start: 33 End: 62 ................................ATTGAAAATGTTGAGATTTAATGATAAAAT........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caaatgtattaaatattataaggtaaagtcttattgaaaatgttgagatttaatgataaaataatagaaatatggtaatttaagattggggaggtaaataaagaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1796:FN1797|FN1796:FN1797:hypothetical protein:Spermidine/putrescine transport ATP-binding protein potA:->->:278856..278960 105 caaatgtattaaatattataaggtaaagtcttattgaaaatgttgagatttaatgataaaataatagaaatatggtaatttaagattggggaggtaaataaagaa Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_003454_FN1796_FN1797|hypothetical protein:Spermidine/putrescine transport ATP-binding protein potA|POSITIVE:POSITIVE|[278856,278960]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 caaatgtattaaatattataaggtaaagtcttattgaaaatgttgagatttaatgataaaataatagaaatatggtaatttaagattggggaggtaaataaagaa caaatgtattaaatattataaggtaaagtcttattgaaaatgttgagatttaatgataaaataatagaaatatggtaatttaagattggggaggtaaataaagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAUGUAUUAAAUAUUAUAAGGUAAAGUCUUAUUGAAAAUGUUGAGAUUUAAUGAUAAAAUAAUAGAAAUAUGGUAAUUUAAGAUUGGGGAGGUAAAUAAAGAA .....(((((...((((((...((.((((((((..........))))))))....))...))))))..)))))................................ ( -8.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUUAUUUACCUCCCCAAUCUUAAAUUACCAUAUUUCUAUUAUUUUAUCAUUAAAUCUCAACAUUUUCAAUAAGACUUUACCUUAUAAUAUUUAAUACAUUUG .......................................................................(((((.......)))))................. ( -1.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 95 54 231 192 NC_003454:FN0814|5end_Propionate_CoA-transferase_1472717..1472947_POSITIVE 208 68 25 45 1 NC_003454:FN0306|5end_Iron(III)_dicitrate_transport_system_permease_protein_fecD_941100..941330_POSITIVE 188 96 55 209 171 NC_003454:FN1882|5end_hypothetical_protein_368560..368790_POSITIVE 184 68 21 80 17 NC_003454:FN0831|5end_Hemin_receptor_1494126..1494356_NEGATIVE 173 94 52 196 155 NC_003454:FN0042|5end_Rod_shape-determining_protein_rodA_682129..682359_NEGATIVE 169 60 12 165 113 NC_003454:FN1651|5end_Oligopeptide_transport_system_permease_protein_oppB_145799..146029_NEGATIVE 162 60 13 225 176 NC_003454:FN0979|5end_hypothetical_protein_1632096..1632326_POSITIVE 161 76 38 55 16 NC_003454:FN1127|5end_Hypothetical_membrane-spanning_protein_1772127..1772357_NEGATIVE 161 95 73 47 23 NC_003454:FN1542|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_56192..56422_POSITIVE 159 87 58 63 34 NC_003454:FN1502|5end_Nickel_transport_system_permease_protein_nikC_7522..7752_NEGATIVE 158 70 21 221 166 NC_003454:FN1845|5end_Ceramide_glucosyltransferase_334387..334617_POSITIVE 156 89 71 202 184 NC_003454:FN1297|5end_Methionine_aminopeptidase_1954981..1955211_NEGATIVE 155 38 6 80 43 NC_003454:FN0128|5end_Spermidine/putrescine-binding_protein_756651..756881_POSITIVE 153 46 1 197 152 NC_003454:FN0535|5end_hypothetical_protein_1189351..1189581_POSITIVE 152 98 70 193 152 NC_003454:FN1435|5end_Export_ABC_transporter_2105034..2105264_POSITIVE 148 57 16 120 76 NC_003454:FN1447|5end_Transposase_2116639..2116869_POSITIVE 148 94 54 231 198 NC_003454:FN0686|5end_Integral_membrane_protein_1342498..1342728_NEGATIVE 148 57 16 120 76 NC_003454:FN1888|5end_Transposase_372411..372641_POSITIVE 147 94 53 80 45 NC_003454:FN1288|5end_hypothetical_protein_1944580..1944810_POSITIVE 146 46 27 88 69 NC_003454:FN0496|5end_hypothetical_protein_1140910..1141140_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 177 78 33 83 39 NC_003454:FN1018|3end_hypothetical_protein_1672145..1672295_NEGATIVE 169 68 22 81 27 NC_003454:FN0051|3end_hypothetical_protein_688783..688933_NEGATIVE 161 95 73 50 26 NC_003454:FN1541|3end_Heptaprenyl_diphosphate_synthase_component_II_56275..56425_POSITIVE 159 87 58 82 53 NC_003454:FN1503|3end_Nickel_transport_system_permease_protein_nikB_7503..7653_NEGATIVE 158 36 11 125 99 NC_003454:FN1271|3end_Protease_IV_1926745..1926895_NEGATIVE 153 46 1 132 87 NC_003454:FN0534|3end_hypothetical_protein_1189366..1189516_POSITIVE 153 94 58 63 28 NC_003454:FN1986|3end_hypothetical_protein_490007..490157_POSITIVE 153 94 83 99 88 NC_003454:FN1705|3end_hypothetical_protein_201464..201614_NEGATIVE 152 98 73 45 12 NC_003454:FN2000|3end_HIPA_protein_501303..501453_POSITIVE 148 48 14 96 57 NC_003454:FN1659|3end_hypothetical_protein_155826..155976_POSITIVE 146 97 74 124 101 NC_003454:FN1952|3end_Na(+)-linked_D-alanine_glycine_permease_458943..459093_NEGATIVE 144 70 21 52 1 NC_003454:FN1516|3end_hypothetical_protein_20664..20814_NEGATIVE 142 80 44 82 46 NC_003454:FN0944|3end_Na+_driven_multidrug_efflux_pump_1597488..1597638_NEGATIVE 142 86 45 134 96 NC_003454:FN0246|3end_hypothetical_protein_870633..870783_NEGATIVE 140 96 63 65 34 NC_003454:FN1302|3end_hypothetical_protein_1959667..1959817_POSITIVE 136 95 61 89 52 NC_003454:FN2082|3end_Formate--tetrahydrofolate_ligase_593257..593407_NEGATIVE 136 40 5 47 7 NC_003454:FN1862|3end_L-beta-lysine_5,6-aminomutase_beta_subunit_352331..352481_NEGATIVE 134 36 2 137 100 NC_003454:FN0225|3end_Gluconate_permease_851715..851865_NEGATIVE 133 95 69 28 2 NC_003454:FN1988|3end_Tyrosine_phenol-lyase_492380..492530_POSITIVE 132 74 33 42 7 NC_003454:FN1549|3end_Stomatin_like_protein_64853..65003_POSITIVE