Origin IGS: ttttattaattacaccagaaatcttatagttaagattaactccttaacttgaccataagataatggtgtttttttattacaaaaaaatactagacacacatttctgtatctagtattcttaactttaaaaaggggtatcaatataatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaattatattgatacccctttttaaagttaagaatactagatacagaaatgtgtgtctagtatttttttgtaataaaaaaacaccattatcttatggtcaagttaaggagttaatcttaactataagatttctggtgtaattaataaaa Mask Tandem Repeat Region ================================================ ttttattaattacaccagaaatcttatagttaagattaactccttaacttgaccataagataatggtgtttttttattacaaaaaaatactagacacacatttctgtatctagtattcttaactttaaaaaggggtatcaatataatttt Find is-nt database================================================ Query_seq: FN1525:FN1526|FN1525:FN1526:Dipeptide transport ATP-binding protein dppF:Fusobacterium outer membrane protein family:-><-:31692..31841 150 ttttattaattacaccagaaatcttatagttaagattaactccttaacttgaccataagataatggtgtttttttattacaaaaaaatactagacacacatttctgtatctagtattcttaactttaaaaaggggtatcaatataatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1525:FN1526|FN1525:FN1526:Dipeptide transport ATP-binding protein dppF:Fusobacterium outer membrane protein family:-><-:31692..31841 150 ttttattaattacaccagaaatcttatagttaagattaactccttaacttgaccataagataatggtgtttttttattacaaaaaaatactagacacacatttctgtatctagtattcttaactttaaaaaggggtatcaatataatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1525:FN1526|FN1525:FN1526:Dipeptide transport ATP-binding protein dppF:Fusobacterium outer membrane protein family:-><-:31692..31841 150 ttttattaattacaccagaaatcttatagttaagattaactccttaacttgaccataagataatggtgtttttttattacaaaaaaatactagacacacatttctgtatctagtattcttaactttaaaaaggggtatcaatataatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttattaattacaccagaaatcttatagttaagattaactccttaacttgaccataagataatggtgtttttttattacaaaaaaatactagacacacatttctgtatctagtattcttaactttaaaaaggggtatcaatataatttt Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: - Start: 13 End: 147 ............ V L F R I T L I L E K V Q G Y S L P T K K N C F F V L C V N R Y R T N K V K F L P I L I M ... ttttattaattacaccagaaatcttatagttaagattaactccttaacttgaccataagataatggtgtttttttattacaaaaaaatactagacacacatttctgtatctagtattcttaactttaaaaaggggtatcaatataatttt 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: 118 End: 147 .....................................................................................................................CTTAACTTTAAAAAGGGGTATCAATATAAT... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 90 End: 119 .........................................................................................CTAGACACACATTTCTGTATCTAGTATTCT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttattaattacaccagaaatcttatagttaagattaactccttaacttgaccataagataatggtgtttttttattacaaaaaaatactagacacacatttctgtatctagtattcttaactttaaaaaggggtatcaatataatttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -7.9 Tail_Score: -5.67063 Start: 88 End: 115 Full_Region: ttttaaagttaagaa tactagataca gaaatg tgtgtctagta tttttttgtaataaa .......................................................................................tactagatacagaaatgtgtgtctagta................................... Find igs database================================================ Query_seq: FN1525:FN1526|FN1525:FN1526:Dipeptide transport ATP-binding protein dppF:Fusobacterium outer membrane protein family:-><-:31692..31841 150 ttttattaattacaccagaaatcttatagttaagattaactccttaacttgaccataagataatggtgtttttttattacaaaaaaatactagacacacatttctgtatctagtattcttaactttaaaaaggggtatcaatataatttt Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: NC_003454_FN1525_FN1526|Dipeptide transport ATP-binding protein dppF:Fusobacterium outer membrane protein family|POSITIVE:NEGATIVE|[31692,31841]|150 HSP 1 e-value: 6.0E-55 bit: 214.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 ttttattaattacaccagaaatcttatagttaagattaactccttaacttgaccataagataatggtgnnnnnnnattacnnnnnnntactagacacacatttctgtatctagtattcttaactttaaaaaggggtatcaatataatttt ttttattaattacaccagaaatcttatagttaagattaactccttaacttgaccataagataatggtgtttttttattacaaaaaaatactagacacacatttctgtatctagtattcttaactttaaaaaggggtatcaatataatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUUAAUUACACCAGAAAUCUUAUAGUUAAGAUUAACUCCUUAACUUGACCAUAAGAUAAUGGUGUUUUUUUAUUACAAAAAAAUACUAGACACACAUUUCUGUAUCUAGUAUUCUUAACUUUAAAAAGGGGUAUCAAUAUAAUUUU ...........((((((...(((((((.((((((.((((....)))))))))).)))))))..))))))(((((((.........(((((((((.(((......))).)))))))))........))))))).................. (-32.73) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUAUAUUGAUACCCCUUUUUAAAGUUAAGAAUACUAGAUACAGAAAUGUGUGUCUAGUAUUUUUUUGUAAUAAAAAAACACCAUUAUCUUAUGGUCAAGUUAAGGAGUUAAUCUUAACUAUAAGAUUUCUGGUGUAAUUAAUAAAA .......(((((((.....((((((.....((((((((((((((((......))))))))))))))))......)))))).((((((..((((((((((.(((((((....)))).))).))))))))))...)))))).)))))))... (-42.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 140 91 139 92 NC_003454:FN1617|5end_Prolipoprotein_diacylglyceryltransferase_126666..126896_NEGATIVE 221 56 12 190 128 NC_003454:FN1929|5end_Competence-damage_protein_cinA_429733..429963_NEGATIVE 210 139 98 220 174 NC_003454:FN1532|5end_murein_hydrolase_exporter_45319..45549_NEGATIVE 199 52 14 196 161 NC_003454:FN1941|5end_ClpB_protein_441279..441509_POSITIVE 197 54 13 61 13 NC_003454:FN0174|5end_Enoyl-[acyl-carrier-protein]_reductase_799427..799657_POSITIVE 194 60 14 121 74 NC_003454:FN0265|5end_Cell_division_protein_ftsX_891404..891634_POSITIVE 193 69 43 179 146 NC_003454:FN1710|5end_Integral_membrane_protein,_YGGT_family_205992..206222_POSITIVE 190 60 15 178 132 NC_003454:FN0045|5end_Shikimate_5-dehydrogenase_683012..683242_POSITIVE 186 139 103 51 12 NC_003454:FN0594|5end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1248785..1249015_POSITIVE 184 60 13 190 139 NC_003454:FN1750|5end_Pyruvate-flavodoxin_oxidoreductase_247811..248041_POSITIVE 183 45 9 84 50 NC_003454:FN1427|5end_Phenazine_biosynthesis_protein_phzF_2095802..2096032_POSITIVE 181 140 93 148 101 NC_003454:FN1749|5end_Pyruvate-flavodoxin_oxidoreductase_247461..247691_POSITIVE 178 68 22 137 86 NC_003454:FN1639|5end_SSU_ribosomal_protein_S3P_138163..138393_NEGATIVE 176 127 101 214 181 NC_003454:FN0849|5end_8-amino-7-oxononanoate_synthase_1507767..1507997_POSITIVE 175 122 103 110 91 NC_003454:FN0443|5end_hypothetical_protein_1082680..1082910_POSITIVE 175 58 26 153 119 NC_003454:FN0202|5end_Glutaconate_CoA-transferase_subunit_A_827780..828010_POSITIVE 175 140 100 47 9 NC_003454:FN0039|5end_DNA_primase_(bacterial_type)_and_small_primase-like_proteins_679212..679442_NEGATIVE 174 83 53 224 190 NC_003454:FN0666|5end_hypothetical_protein_1321599..1321829_POSITIVE 174 48 7 110 67 NC_003454:FN0176|5end_Cell_division_inhibitor_MinD_801157..801387_POSITIVE 173 79 32 50 3 NC_003454:FN0634|5end_GTP-binding_protein_TypA/BipA_1294107..1294337_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 140 91 139 92 NC_003454:FN1618|3end_hypothetical_protein_126666..126816_NEGATIVE 243 69 21 79 30 NC_003454:FN1525|3end_Dipeptide_transport_ATP-binding_protein_dppF_31631..31781_POSITIVE 233 79 32 90 33 NC_003454:FN1463|3end_pyridoxine_biosynthesis_protein_2145924..2146074_POSITIVE 198 70 23 56 3 NC_003454:FN0670|3end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1326699..1326849_POSITIVE 190 60 15 127 81 NC_003454:FN0044|3end_Shikimate_5-dehydrogenase_683041..683191_POSITIVE 178 68 22 118 67 NC_003454:FN1640|3end_LSU_ribosomal_protein_L22P_138182..138332_NEGATIVE 176 127 101 130 97 NC_003454:FN0848|3end_hypothetical_protein_1507763..1507913_POSITIVE 175 58 26 42 8 NC_003454:FN0201|3end_Glutaconyl-COA_decarboxylase_beta_subunit_827749..827899_POSITIVE 174 48 7 108 65 NC_003454:FN0175|3end_Cell_division_inhibitor_MinC_801235..801385_POSITIVE 166 76 39 119 79 NC_003454:FN0230|3end_hypothetical_protein_856519..856669_NEGATIVE 165 141 105 128 101 NC_003454:FN1661|3end_Hypothetical_cytosolic_protein_157963..158113_NEGATIVE 164 136 102 59 17 NC_003454:FN0657|3end_Acetyltransferase_1314867..1315017_POSITIVE 164 37 8 70 43 NC_003454:FN0289|3end_hypothetical_protein_915886..916036_NEGATIVE 164 136 91 58 12 NC_003454:FN1973|3end_Translation_initiation_inhibitor_472230..472380_NEGATIVE 163 74 40 109 80 NC_003454:FN1280|3end_Endonuclease_1940261..1940411_POSITIVE 162 44 2 74 35 NC_003454:FN1846|3end_hypothetical_protein_336225..336375_POSITIVE 162 44 14 148 124 NC_003454:FN1548|3end_hypothetical_protein_63950..64100_POSITIVE 161 150 102 100 56 NC_003454:FN1983|3end_Alkyl_hydroperoxide_reductase_C22_protein_485265..485415_POSITIVE 160 121 89 123 94 NC_003454:FN0589|3end_Transcriptional_regulator,_MarR_family_1242833..1242983_POSITIVE 159 78 31 79 31 NC_003454:FN0831|3end_Hemin_receptor_1492030..1492180_NEGATIVE