Origin IGS: tataaaaaaagttcattattagataaatttttcttgaaatatagttatttaaaatttttgtatcttgtgcaaactgcttgatagccattagtgtttcgtgagctccacaaaggctccctcaacaataatggacatcgcagcagttttatttaaaaattatttaatgctgctttcaagaaaaattataactcacttatttttatattatatagtatgaggaa .........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 ttcctcatactatataatataaaaataagtgagttataatttttcttgaaagcagcattaaataatttttaaataaaactgctgcgatgtccattattgttgagggagcctttgtggagctcacgaaacactaatggctatcaagcagtttgcacaagatacaaaaattttaaataactatatttcaagaaaaatttatctaataatgaactttttttata Mask Tandem Repeat Region ================================================ tataaaaaaagttcattattagataaatttttcttgaaatatagttatttaaaatttttgtatcttgtgcaaactgcttgatagccattagtgtttcgtgagctccacaaaggctccctcaacaataatggacatcgcagcagttttatttaaaaattatttaatgctgctttcaagaaaaattataactcacttatttttatattatatagtatgaggaa Find is-nt database================================================ Query_seq: FN0053:FN0054|FN0053:FN0054:Branched-chain amino acid transport system carrier protein:tyrosyl-tRNA synthetase:->->:690755..690975 221 tataaaaaaagttcattattagataaatttttcttgaaatatagttatttaaaatttttgtatcttgtgcaaactgcttgatagccattagtgtttcgtgagctccacaaaggctccctcaacaataatggacatcgcagcagttttatttaaaaattatttaatgctgctttcaagaaaaattataactcacttatttttatattatatagtatgaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0053:FN0054|FN0053:FN0054:Branched-chain amino acid transport system carrier protein:tyrosyl-tRNA synthetase:->->:690755..690975 221 tataaaaaaagttcattattagataaatttttcttgaaatatagttatttaaaatttttgtatcttgtgcaaactgcttgatagccattagtgtttcgtgagctccacaaaggctccctcaacaataatggacatcgcagcagttttatttaaaaattatttaatgctgctttcaagaaaaattataactcacttatttttatattatatagtatgaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0053:FN0054|FN0053:FN0054:Branched-chain amino acid transport system carrier protein:tyrosyl-tRNA synthetase:->->:690755..690975 221 tataaaaaaagttcattattagataaatttttcttgaaatatagttatttaaaatttttgtatcttgtgcaaactgcttgatagccattagtgtttcgtgagctccacaaaggctccctcaacaataatggacatcgcagcagttttatttaaaaattatttaatgctgctttcaagaaaaattataactcacttatttttatattatatagtatgaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataaaaaaagttcattattagataaatttttcttgaaatatagttatttaaaatttttgtatcttgtgcaaactgcttgatagccattagtgtttcgtgagctccacaaaggctccctcaacaataatggacatcgcagcagttttatttaaaaattatttaatgctgctttcaagaaaaattataactcacttatttttatattatatagtatgaggaa Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 98 End: 214 ................................................................................................. M S S T K A P S T I M D I A A V L F K N Y L M L L S R K I I T H L F L Y Y I V ....... Protein_Len: 34 Strand: - Start: 48 End: 149 ............................................... K F N K Y R T C V A Q Y G N T N R S S W L P E R L L L P C R L L K M ........................................................................ tataaaaaaagttcattattagataaatttttcttgaaatatagttatttaaaatttttgtatcttgtgcaaactgcttgatagccattagtgtttcgtgagctccacaaaggctccctcaacaataatggacatcgcagcagttttatttaaaaattatttaatgctgctttcaagaaaaattataactcacttatttttatattatatagtatgaggaa 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================================================ tataaaaaaagttcattattagataaatttttcttgaaatatagttatttaaaatttttgtatcttgtgcaaactgcttgatagccattagtgtttcgtgagctccacaaaggctccctcaacaataatggacatcgcagcagttttatttaaaaattatttaatgctgctttcaagaaaaattataactcacttatttttatattatatagtatgaggaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0053:FN0054|FN0053:FN0054:Branched-chain amino acid transport system carrier protein:tyrosyl-tRNA synthetase:->->:690755..690975 221 tataaaaaaagttcattattagataaatttttcttgaaatatagttatttaaaatttttgtatcttgtgcaaactgcttgatagccattagtgtttcgtgagctccacaaaggctccctcaacaataatggacatcgcagcagttttatttaaaaattatttaatgctgctttcaagaaaaattataactcacttatttttatattatatagtatgaggaa Intra-Species Hit: Count: 1 Min: 11 Max: 221 Len: 211 Subject: NC_003454_FN0053_FN0054|Branched-chain amino acid transport system carrier protein:tyrosyl-tRNA synthetase|POSITIVE:POSITIVE|[690755,690975]|221 HSP 1 e-value: 1.0E-116 bit: 418.0 Len: 211 Query Start:11 Query End:221 Subject Strand: POSITIVE Subject Start: 11 Subject End: 221 ..........gttcattattagataaatttttcttgaaatatagttatttaaaatttttgtatcttgtgcaaactgcttgatagccattagtgtttcgtgagctccacaaaggctccctcaacaataatggacatcgcagcagttttatttaaaaattatttaatgctgctttcaagaaaaattataactcacttatttttatattatatagtatgaggaa ..........gttcattattagataaatttttcttgaaatatagttatttaaaatttttgtatcttgtgcaaactgcttgatagccattagtgtttcgtgagctccacaaaggctccctcaacaataatggacatcgcagcagttttatttaaaaattatttaatgctgctttcaagaaaaattataactcacttatttttatattatatagtatgaggaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUCAUUAUUAGAUAAAUUUUUCUUGAAAUAUAGUUAUUUAAAAUUUUUGUAUCUUGUGCAAACUGCUUGAUAGCCAUUAGUGUUUCGUGAGCUCCACAAAGGCUCCCUCAACAAUAAUGGACAUCGCAGCAGUUUUAUUUAAAAAUUAUUUAAUGCUGCUUUCAAGAAAAAUUAUAACUCACUUAUUUUUAUAUUAUAUAGUAUGAGGAA ...............((((((((((((((..((((...((((((((((((......(((.((((((((((((..((((((.((((..(.(((((.......))))).)..)))).))))))..)))).))))))))))).)))))))..))))).)))).))))))))))))))............((((((((((....)))))))))). (-51.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUCAUACUAUAUAAUAUAAAAAUAAGUGAGUUAUAAUUUUUCUUGAAAGCAGCAUUAAAUAAUUUUUAAAUAAAACUGCUGCGAUGUCCAUUAUUGUUGAGGGAGCCUUUGUGGAGCUCACGAAACACUAAUGGCUAUCAAGCAGUUUGCACAAGAUACAAAAAUUUUAAAUAACUAUAUUUCAAGAAAAAUUUAUCUAAUAAUGAAC ...(((((....................)))))....((((((((((((((...((.(((((.....)))))...((((((((..((((.((((((.((((..(.((((((....)).)))).)..)))).)))))).)))).))))))))))..(((((......)))))...........))))))))))))))............... (-48.95) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 521 120 72 170 122 NC_003454:FN0695|5end_ABC_transporter_ATP-binding_protein_1352886..1353116_POSITIVE 345 140 91 224 176 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 315 100 51 134 83 NC_003454:FN0418|5end_pyrimidine_regulatory_protein_PyrR_1059118..1059348_POSITIVE 294 104 65 228 192 NC_003454:FN0481|5end_hypothetical_protein_1127777..1128007_POSITIVE 279 137 91 52 8 NC_003454:FN1253|5end_hypothetical_protein_1910405..1910635_NEGATIVE 268 135 91 65 30 NC_003454:FN1744|5end_Transporter_242920..243150_NEGATIVE 251 97 55 74 29 NC_003454:FN1019|5end_3-hydroxybutyryl-CoA_dehydrogenase_1673784..1674014_NEGATIVE 251 93 63 206 176 NC_003454:FN0220|5end_Autolysin_sensor_kinase_844934..845164_NEGATIVE 242 98 52 123 64 NC_003454:FN2047|5end_Fusobacterium_outer_membrane_protein_family_556383..556613_NEGATIVE 240 125 81 78 32 NC_003454:FN0535|5end_hypothetical_protein_1189351..1189581_POSITIVE 237 119 72 68 7 NC_003454:FN1620|5end_30S_ribosomal_protein_S2_127896..128126_POSITIVE 234 93 59 174 143 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 234 93 59 70 39 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 234 158 122 177 128 NC_003454:FN0606|5end_Translation_initiation_inhibitor_1261014..1261244_POSITIVE 232 100 53 66 17 NC_003454:FN0007|5end_glucose-inhibited_division_protein_A_645938..646168_POSITIVE 225 115 72 75 14 NC_003454:FN0383|5end_Lipopolysaccharide_N-acetylglucosaminyltransferase_1014148..1014378_POSITIVE 224 94 51 125 70 NC_003454:FN1003|5end_Outer_membrane_protein_P1_precursor_1658822..1659052_POSITIVE 223 105 63 223 166 NC_003454:FN1142|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1791529..1791759_POSITIVE 219 104 61 231 170 NC_003454:FN1581|5end_DNA_mismatch_repair_protein_mutS_93231..93461_NEGATIVE 218 110 68 190 135 NC_003454:FN0727|5end_hypothetical_protein_1385507..1385737_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 662 140 91 56 7 NC_003454:FN1260|3end_Sensory_Transduction_Protein_Kinase_1915863..1916013_NEGATIVE 521 120 72 68 20 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 399 140 91 74 26 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 345 140 91 91 43 NC_003454:FN2092|3end_Integral_membrane_protein_602614..602764_NEGATIVE 261 107 65 43 2 NC_003454:FN1076|3end_hypothetical_protein_1723677..1723827_POSITIVE 251 97 55 58 13 NC_003454:FN1020|3end_3-hydroxybutyryl-CoA_dehydratase_1673800..1673950_NEGATIVE 250 135 98 32 1 NC_003454:FN1745|3end_Cystathionine_gamma-synthase_242953..243103_NEGATIVE 249 140 99 88 37 NC_003454:FN1340|3end_Glutamyl-tRNA_synthetase_1993353..1993503_NEGATIVE 234 117 75 142 113 NC_003454:FN1253|3end_hypothetical_protein_1910229..1910379_NEGATIVE 230 143 101 70 16 NC_003454:FN0371|3end_hypothetical_protein_1000840..1000990_POSITIVE 225 115 72 71 10 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 212 88 45 61 12 NC_003454:FN0251|3end_Hypothetical_membrane-spanning_Protein_874256..874406_POSITIVE 212 88 45 61 12 NC_003454:FN2061|3end_Hypothetical_membrane-spanning_protein_573666..573816_NEGATIVE 212 88 45 61 12 NC_003454:FN2050|3end_Hypothetical_membrane-spanning_protein_559590..559740_NEGATIVE 211 94 71 151 125 NC_003454:FN1309|3end_hypothetical_protein_1965130..1965280_POSITIVE 210 109 68 138 77 NC_003454:FN1752|3end_Regulatory_protein_TENI_248591..248741_NEGATIVE 209 125 87 91 46 NC_003454:FN2108|3end_galactose-1-phosphate_uridylyltransferase_620928..621078_POSITIVE 206 89 43 150 112 NC_003454:FN0947|3end_hypothetical_protein_1601349..1601499_POSITIVE 204 137 93 74 22 NC_003454:FN2100|3end_hypothetical_protein_610316..610466_POSITIVE 203 106 63 51 8 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE