Origin IGS: aaaaatcaactcctttatttttatattataagtgattttttcacttttttcaatttatttttattttaattattataaaaagtaaagaaggtcagtataatagggtagaactcttctattatactaaccttcttctgggaaataataatctatattacactagtgttagtgatatattta .........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 taaatatatcactaacactagtgtaatatagattattatttcccagaagaaggttagtataatagaagagttctaccctattatactgaccttctttactttttataataattaaaataaaaataaattgaaaaaagtgaaaaaatcacttataatataaaaataaaggagttgattttt Mask Tandem Repeat Region ================================================ aaaaatcaactcctttatttttatattataagtgattttttcacttttttcaatttatttttattttaattattataaaaagtaaagaaggtcagtataatagggtagaactcttctattatactaaccttcttctgggaaataataatctatattacactagtgttagtgatatattta Find is-nt database================================================ Query_seq: FN1553:FN1554|FN1553:FN1554:Transporter:Fusobacterium outer membrane protein family:<-<-:68629..68808 180 aaaaatcaactcctttatttttatattataagtgattttttcacttttttcaatttatttttattttaattattataaaaagtaaagaaggtcagtataatagggtagaactcttctattatactaaccttcttctgggaaataataatctatattacactagtgttagtgatatattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1553:FN1554|FN1553:FN1554:Transporter:Fusobacterium outer membrane protein family:<-<-:68629..68808 180 aaaaatcaactcctttatttttatattataagtgattttttcacttttttcaatttatttttattttaattattataaaaagtaaagaaggtcagtataatagggtagaactcttctattatactaaccttcttctgggaaataataatctatattacactagtgttagtgatatattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1553:FN1554|FN1553:FN1554:Transporter:Fusobacterium outer membrane protein family:<-<-:68629..68808 180 aaaaatcaactcctttatttttatattataagtgattttttcacttttttcaatttatttttattttaattattataaaaagtaaagaaggtcagtataatagggtagaactcttctattatactaaccttcttctgggaaataataatctatattacactagtgttagtgatatattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaatcaactcctttatttttatattataagtgattttttcacttttttcaatttatttttattttaattattataaaaagtaaagaaggtcagtataatagggtagaactcttctattatactaaccttcttctgggaaataataatctatattacactagtgttagtgatatattta Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 57 End: 179 ........................................................ M F I L I I I K S K E G Q Y N R V E L F Y Y T N L L L G N N N L Y Y T S V S D I F . aaaaatcaactcctttatttttatattataagtgattttttcacttttttcaatttatttttattttaattattataaaaagtaaagaaggtcagtataatagggtagaactcttctattatactaaccttcttctgggaaataataatctatattacactagtgttagtgatatattta 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: 89 Start: 25 End: 54 ........................ATTGAAAAAAGTGAAAAAATCACTTATAAT.............................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 47 End: 76 ..............................................TTTTCAATTTATTTTTATTTTAATTATTAT........................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaatcaactcctttatttttatattataagtgattttttcacttttttcaatttatttttattttaattattataaaaagtaaagaaggtcagtataatagggtagaactcttctattatactaaccttcttctgggaaataataatctatattacactagtgttagtgatatattta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -10.7 Tail_Score: -3.30441 Start: 87 End: 132 Full_Region: ATTATAAAAAGTAAA GAAGGTCAGTATAATAGGGTA GAAC TCTTCTATTATACTAACCTTC TTCTGGGAAATAATA ......................................................................................GAAGGTCAGTATAATAGGGTAGAACTCTTCTATTATACTAACCTTC................................................ TransTerm Strand: - Conf: 87 HP_score: -10.1 Tail_Score: -4.3902 Start: 87 End: 132 Full_Region: tattatttcccagaa gaaggttagtataatag aagagttctacc ctattatactgaccttc tttactttttataat ......................................................................................gaaggttagtataatagaagagttctaccctattatactgaccttc................................................ Find igs database================================================ Query_seq: FN1553:FN1554|FN1553:FN1554:Transporter:Fusobacterium outer membrane protein family:<-<-:68629..68808 180 aaaaatcaactcctttatttttatattataagtgattttttcacttttttcaatttatttttattttaattattataaaaagtaaagaaggtcagtataatagggtagaactcttctattatactaaccttcttctgggaaataataatctatattacactagtgttagtgatatattta Intra-Species Hit: Count: 1 Min: 77 Max: 180 Len: 104 Subject: NC_003454_FN1553_FN1554|Transporter:Fusobacterium outer membrane protein family|NEGATIVE:NEGATIVE|[68629,68808]|180 HSP 1 e-value: 2.0E-52 bit: 206.0 Len: 104 Query Start:77 Query End:180 Subject Strand: POSITIVE Subject Start: 77 Subject End: 180 ............................................................................aaaaagtaaagaaggtcagtataatagggtagaactcttctattatactaaccttcttctgggaaataataatctatattacactagtgttagtgatatattta ............................................................................aaaaagtaaagaaggtcagtataatagggtagaactcttctattatactaaccttcttctgggaaataataatctatattacactagtgttagtgatatattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAGUAAAGAAGGUCAGUAUAAUAGGGUAGAACUCUUCUAUUAUACUAACCUUCUUCUGGGAAAUAAUAAUCUAUAUUACACUAGUGUUAGUGAUAUAUUUA ........((((((((.((((((((((((........)))))))))))).))))))))................((((((((((....))..)))))))).... (-27.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUAUAUCACUAACACUAGUGUAAUAUAGAUUAUUAUUUCCCAGAAGAAGGUUAGUAUAAUAGAAGAGUUCUACCCUAUUAUACUGACCUUCUUUACUUUUU ....((((((((((....)))))..)))))...............((((((((((((((((((((.((....))...))))))))))))))))))))....... (-31.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 816 60 11 227 178 NC_003454:FN1553|5end_Transporter_68538..68768_NEGATIVE 443 95 57 185 142 NC_003454:FN1891|5end_Glycerophosphoryl_diester_phosphodiesterase_374294..374524_NEGATIVE 242 49 10 197 144 NC_003454:FN0312|5end_Anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_949316..949546_POSITIVE 238 55 12 164 121 NC_003454:FN1087|5end_hypothetical_protein_1730958..1731188_POSITIVE 225 67 35 231 195 NC_003454:FN1261|5end_Two-component_response_regulator_1917871..1918101_NEGATIVE 219 70 38 96 64 NC_003454:FN2057|5end_hypothetical_protein_565624..565854_NEGATIVE 218 79 36 93 53 NC_003454:FN0743|5end_ATP-dependent_helicase,_DinG_family_1400850..1401080_POSITIVE 209 97 52 104 66 NC_003454:FN0666|5end_hypothetical_protein_1321599..1321829_POSITIVE 204 97 54 64 20 NC_003454:FN1993|5end_SUA5_protein_496917..497147_POSITIVE 199 50 10 74 30 NC_003454:FN1920|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_416910..417140_NEGATIVE 197 64 21 60 20 NC_003454:FN0332|5end_Magnesium_and_cobalt_transport_protein_corA_967230..967460_NEGATIVE 197 68 25 68 4 NC_003454:FN0006|5end_tRNA_modification_GTPase_644505..644735_POSITIVE 196 79 39 208 164 NC_003454:FN0397|5end_Dipeptide_transport_system_permease_protein_dppB_1035822..1036052_POSITIVE 195 65 33 66 32 NC_003454:FN0127|5end_Fe-S_oxidoreductase_756312..756542_NEGATIVE 194 49 3 210 158 NC_003454:FN1474|5end_N-acetylmannosamine_kinase_2156888..2157118_POSITIVE 193 42 4 107 66 NC_003454:FN1549|5end_Stomatin_like_protein_63889..64119_POSITIVE 192 96 53 76 39 NC_003454:FN1190|5end_Probable_cadmium-transporting_ATPase_1851677..1851907_POSITIVE 192 60 22 94 52 NC_003454:FN0156|5end_Phosphopantetheine_adenylyltransferase_784403..784633_POSITIVE 189 42 2 164 128 NC_003454:FN0590|5end_N-acyl-L-amino_acid_amidohydrolase_1244037..1244267_NEGATIVE 189 49 14 231 191 NC_003454:FN1736|5end_V-type_sodium_ATP_synthase_subunit_A_236021..236251_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 513 95 51 73 30 NC_003454:FN1449|3end_Fusobacterium_outer_membrane_protein_family_2118612..2118762_NEGATIVE 443 95 57 67 24 NC_003454:FN1893|3end_Fusobacterium_outer_membrane_protein_family_374412..374562_NEGATIVE 227 63 33 148 118 NC_003454:FN1265|3end_Outer_membrane_protein_1922019..1922169_POSITIVE 209 97 52 51 13 NC_003454:FN0665|3end_N-acetylmuramoyl-L-alanine_amidase_1321626..1321776_POSITIVE 207 44 7 145 106 NC_003454:FN0047|3end_Exodeoxyribonuclease_III_685268..685418_POSITIVE 204 97 54 62 18 NC_003454:FN1992|3end_Ribose-phosphate_pyrophosphokinase_496995..497145_POSITIVE 200 60 18 60 15 NC_003454:FN0023|3end_Short-chain_fatty_acids_transporter_662780..662930_POSITIVE 199 50 10 74 30 NC_003454:FN1921|3end_Biotin_operon_repressor_416910..417060_NEGATIVE 197 64 21 43 3 NC_003454:FN0333|3end_Glycerol_uptake_operon_antiterminator_regulatory_protein_967247..967397_NEGATIVE 196 79 39 124 80 NC_003454:FN0396|3end_Dipeptide-binding_protein_1035818..1035968_POSITIVE 195 68 26 62 2 NC_003454:FN0005|3end_Jag_protein_644579..644729_POSITIVE 193 42 4 88 47 NC_003454:FN1548|3end_hypothetical_protein_63950..64100_POSITIVE 192 96 53 69 32 NC_003454:FN1189|3end_hypothetical_protein_1851750..1851900_POSITIVE 192 60 22 73 31 NC_003454:FN0155|3end_hypothetical_protein_784462..784612_POSITIVE 189 42 2 148 112 NC_003454:FN0591|3end_Putative_efflux_pump_component_MtrF_1244053..1244203_NEGATIVE 188 55 17 149 108 NC_003454:FN0790|3end_Xylose_repressor_1445294..1445444_NEGATIVE 184 45 4 54 3 NC_003454:FN0695|3end_ABC_transporter_ATP-binding_protein_1353691..1353841_POSITIVE 182 75 53 145 123 NC_003454:FN1144|3end_hypothetical_protein_1793403..1793553_NEGATIVE 180 98 73 55 30 NC_003454:FN1561|3end_Hypothetical_cytosolic_protein_83032..83182_NEGATIVE 179 99 54 62 21 NC_003454:FN1837|3end_putative_nucleotide-binding_protein_326725..326875_NEGATIVE