Origin IGS: aatttcttcttcaagaattttaaggactttttcaattttagtttccattttatcccccttataaatttaattttatagtacattataaaataaatttttaaaaaagtacaccctcttcaaaaaaaatatgttcataataatatttacgattttttatgttgctttttgtttgagaaaagtatataatttaggaaagaaataaactttattatagtctatatggaggaatact .........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 agtattcctccatatagactataataaagtttatttctttcctaaattatatacttttctcaaacaaaaagcaacataaaaaatcgtaaatattattatgaacatattttttttgaagagggtgtacttttttaaaaatttattttataatgtactataaaattaaatttataagggggataaaatggaaactaaaattgaaaaagtccttaaaattcttgaagaagaaatt Mask Tandem Repeat Region ================================================ aatttcttcttcaagaattttaaggactttttcaattttagtttccattttatcccccttataaatttaattttatagtacattataaaataaatttttaaaaaagtacaccctcttcaaaaaaaatatgttcataataatatttacgattttttatgttgctttttgtttgagaaaagtatataatttaggaaagaaataaactttattatagtctatatggaggaatact Find is-nt database================================================ Query_seq: FN1147:FN1148|FN1147:FN1148:hypothetical protein:Serine/threonine sodium symporter:<-->:1797920..1798151 232 aatttcttcttcaagaattttaaggactttttcaattttagtttccattttatcccccttataaatttaattttatagtacattataaaataaatttttaaaaaagtacaccctcttcaaaaaaaatatgttcataataatatttacgattttttatgttgctttttgtttgagaaaagtatataatttaggaaagaaataaactttattatagtctatatggaggaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1147:FN1148|FN1147:FN1148:hypothetical protein:Serine/threonine sodium symporter:<-->:1797920..1798151 232 aatttcttcttcaagaattttaaggactttttcaattttagtttccattttatcccccttataaatttaattttatagtacattataaaataaatttttaaaaaagtacaccctcttcaaaaaaaatatgttcataataatatttacgattttttatgttgctttttgtttgagaaaagtatataatttaggaaagaaataaactttattatagtctatatggaggaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1147:FN1148|FN1147:FN1148:hypothetical protein:Serine/threonine sodium symporter:<-->:1797920..1798151 232 aatttcttcttcaagaattttaaggactttttcaattttagtttccattttatcccccttataaatttaattttatagtacattataaaataaatttttaaaaaagtacaccctcttcaaaaaaaatatgttcataataatatttacgattttttatgttgctttttgtttgagaaaagtatataatttaggaaagaaataaactttattatagtctatatggaggaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttcttcttcaagaattttaaggactttttcaattttagtttccattttatcccccttataaatttaattttatagtacattataaaataaatttttaaaaaagtacaccctcttcaaaaaaaatatgttcataataatatttacgattttttatgttgctttttgtttgagaaaagtatataatttaggaaagaaataaactttattatagtctatatggaggaatact Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 94 End: 183 ............................................................................................. M F K K V H P L Q K K Y V H N N I Y D F L C C F L F E K S I ................................................. Protein_Len: 31 Strand: - Start: 3 End: 95 .. K K K L F K L S K K L K L K W K I G R I F K I K Y Y M I F Y M ......................................................................................................................................... aatttcttcttcaagaattttaaggactttttcaattttagtttccattttatcccccttataaatttaattttatagtacattataaaataaatttttaaaaaagtacaccctcttcaaaaaaaatatgttcataataatatttacgattttttatgttgctttttgtttgagaaaagtatataatttaggaaagaaataaactttattatagtctatatggaggaatact 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: 85 Start: 158 End: 187 .............................................................................................................................................................GTTGCTTTTTGTTTGAGAAAAGTATATAAT............................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 82 End: 111 .................................................................................GTGTACTTTTTTAAAAATTTATTTTATAAT......................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatttcttcttcaagaattttaaggactttttcaattttagtttccattttatcccccttataaatttaattttatagtacattataaaataaatttttaaaaaagtacaccctcttcaaaaaaaatatgttcataataatatttacgattttttatgttgctttttgtttgagaaaagtatataatttaggaaagaaataaactttattatagtctatatggaggaatact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 40 HP_score: -2.3 Tail_Score: -3.32997 Start: 71 End: 90 Full_Region: ttttttaaaaattta ttttata atgtac tataaaa ttaaatttataaggg ......................................................................ttttataatgtactataaaa.............................................................................................................................................. Find igs database================================================ Query_seq: FN1147:FN1148|FN1147:FN1148:hypothetical protein:Serine/threonine sodium symporter:<-->:1797920..1798151 232 aatttcttcttcaagaattttaaggactttttcaattttagtttccattttatcccccttataaatttaattttatagtacattataaaataaatttttaaaaaagtacaccctcttcaaaaaaaatatgttcataataatatttacgattttttatgttgctttttgtttgagaaaagtatataatttaggaaagaaataaactttattatagtctatatggaggaatact Intra-Species Hit: Count: 1 Min: 76 Max: 232 Len: 157 Subject: NC_003454_FN1147_FN1148|hypothetical protein:Serine/threonine sodium symporter|NEGATIVE:POSITIVE|[1797920,1798151]|232 HSP 1 e-value: 1.0E-69 bit: 264.0 Len: 157 Query Start:76 Query End:232 Subject Strand: POSITIVE Subject Start: 76 Subject End: 232 ...........................................................................tagtacattataaaataaatttttaaaaaagtacaccctcttcnnnnnnnntatgttcataataatatttacgattttttatgttgctttttgtttgagaaaagtatataatttaggaaagaaataaactttattatagtctatatggaggaatact ...........................................................................tagtacattataaaataaatttttaaaaaagtacaccctcttcaaaaaaaatatgttcataataatatttacgattttttatgttgctttttgtttgagaaaagtatataatttaggaaagaaataaactttattatagtctatatggaggaatact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUACAUUAUAAAAUAAAUUUUUAAAAAAGUACACCCUCUUCAAAAAAAAUAUGUUCAUAAUAAUAUUUACGAUUUUUUAUGUUGCUUUUUGUUUGAGAAAAGUAUAUAAUUUAGGAAAGAAAUAAACUUUAUUAUAGUCUAUAUGGAGGAAUACU ..((((....(((((.....))))).....))))..(((((.........(((((..((((((((..((((...(((((((...((((((((......)))))))).......)))))))....))))..))))))).)..))))))))))...... (-22.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUUCCUCCAUAUAGACUAUAAUAAAGUUUAUUUCUUUCCUAAAUUAUAUACUUUUCUCAAACAAAAAGCAACAUAAAAAAUCGUAAAUAUUAUUAUGAACAUAUUUUUUUUGAAGAGGGUGUACUUUUUUAAAAAUUUAUUUUAUAAUGUACUA (((((........(((((((.......))))))).........................................((((((..((((((......))))))........((((((((((((.....))))))))))))....))))))...))))). (-18.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 610 50 1 216 167 NC_003454:FN1147|5end_hypothetical_protein_1797829..1798059_NEGATIVE 205 45 6 134 101 NC_003454:FN0285|5end_RNA_binding_protein_914171..914401_NEGATIVE 204 109 69 205 164 NC_003454:FN0077|5end_Ethanolamine_two-component_sensor_kinase_714704..714934_POSITIVE 201 119 71 165 107 NC_003454:FN1715|5end_ATPase_211040..211270_POSITIVE 195 94 51 190 143 NC_003454:FN1165|5end_D-galactose-binding_protein_1822898..1823128_POSITIVE 187 90 48 201 164 NC_003454:FN0457|5end_hypothetical_protein_1103298..1103528_POSITIVE 183 104 74 226 197 NC_003454:FN0859|5end_hypothetical_protein_1521229..1521459_NEGATIVE 183 95 52 229 187 NC_003454:FN2105|5end_Integral_membrane_protein_614701..614931_POSITIVE 180 92 67 154 131 NC_003454:FN0343|5end_hypothetical_protein_976653..976883_NEGATIVE 179 143 119 66 43 NC_003454:FN1412|5end_5-methylthioribose_kinase_2073206..2073436_NEGATIVE 173 112 78 94 66 NC_003454:FN1319|5end_DNA_primase_1974197..1974427_NEGATIVE 171 42 2 101 66 NC_003454:FN0537|5end_Hypothetical_membrane-spanning_protein_1191753..1191983_NEGATIVE 164 48 4 110 68 NC_003454:FN0487|5end_D-lactate_dehydrogenase_1132772..1133002_NEGATIVE 164 95 66 32 4 NC_003454:FN0156|5end_Phosphopantetheine_adenylyltransferase_784403..784633_POSITIVE 164 94 62 219 184 NC_003454:FN1729|5end_4-amino-4-deoxychorismate_lyase_229087..229317_NEGATIVE 158 108 61 77 26 NC_003454:FN0472|5end_flavodoxin_1118165..1118395_NEGATIVE 158 79 36 156 101 NC_003454:FN1898|5end_Sugar_transport_ATP-binding_protein_386569..386799_NEGATIVE 155 80 35 150 99 NC_003454:FN0221|5end_Carbon_starvation_protein_A_845209..845439_POSITIVE 155 133 94 146 105 NC_003454:FN0115|5end_hypothetical_protein_748511..748741_NEGATIVE 154 100 62 57 15 NC_003454:FN1764|5end_Enolase_257997..258227_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 205 45 6 122 89 NC_003454:FN0286|3end_hypothetical_protein_914183..914333_NEGATIVE 201 119 71 81 23 NC_003454:FN1714|3end_hypothetical_protein_211036..211186_POSITIVE 183 104 74 149 120 NC_003454:FN0860|3end_hypothetical_protein_1521306..1521456_NEGATIVE 179 143 119 51 28 NC_003454:FN1413|3end_translation_initiation_factor_IF-2B_subunit_alpha_2073221..2073371_NEGATIVE 173 112 78 30 2 NC_003454:FN1320|3end_Peptidyl-prolyl_cis-trans_isomerase_1974261..1974411_NEGATIVE 161 118 71 124 77 NC_003454:FN0018|3end_hypothetical_protein_655978..656128_NEGATIVE 159 111 75 141 107 NC_003454:FN0572|3end_hypothetical_protein_1222337..1222487_NEGATIVE 156 150 102 65 29 NC_003454:FN1987|3end_Transcriptional_regulator,_GntR_family_490018..490168_NEGATIVE 155 38 7 68 31 NC_003454:FN1680|3end_Transposase_175971..176121_NEGATIVE 152 102 65 38 1 NC_003454:FN0624|3end_NA+/H+_antiporter_NHAC_1282995..1283145_NEGATIVE 152 97 52 116 65 NC_003454:FN0576|3end_D-amino_acid_dehydrogenase_large_subunit_1227302..1227452_POSITIVE 150 110 66 131 92 NC_003454:FN1897|3end_ABC_transporter_integral_membrane_protein_383965..384115_NEGATIVE 147 115 72 115 63 NC_003454:FN1281|3end_Cysteine_protease_1941242..1941392_POSITIVE 147 97 60 97 61 NC_003454:FN0611|3end_Threonyl-tRNA_synthetase_1270301..1270451_POSITIVE 146 115 82 93 57 NC_003454:FN0966|3end_Precorrin-6Y_C5,15-methyltransferase_[decarboxylating]_1619280..1619430_NEGATIVE 145 72 37 119 87 NC_003454:FN0385|3end_hypothetical_protein_1018920..1019070_POSITIVE 144 96 67 145 111 NC_003454:FN1677|3end_Transposase_174069..174219_NEGATIVE 143 108 71 56 22 NC_003454:FN0725|3end_Molybdopterin_biosynthesis_MoeB_protein_1384181..1384331_NEGATIVE 143 107 81 42 16 NC_003454:FN0013|3end_Transporter_652639..652789_POSITIVE 142 98 72 54 21 NC_003454:FN0920|3end_Protease_HTPX_1574618..1574768_NEGATIVE