Origin IGS: ttttctttcatagatatcaactattgaatttttatcaactgttcttgttgcactttcttctggaatatctttaacatcttctgtgtttttagcagtttctacacttttttcttttgttgcttttttttctgtttttcctcctactatttcattggaaatttggtcaagtgactcaacttcttttatttcagcactcaataaagaaaagttaaataatactcctgctaaaataaaaaacttagtaaatttgttcattgttttgttctccta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taggagaacaaaacaatgaacaaatttactaagttttttattttagcaggagtattatttaacttttctttattgagtgctgaaataaaagaagttgagtcacttgaccaaatttccaatgaaatagtaggaggaaaaacagaaaaaaaagcaacaaaagaaaaaagtgtagaaactgctaaaaacacagaagatgttaaagatattccagaagaaagtgcaacaagaacagttgataaaaattcaatagttgatatctatgaaagaaaa Mask Tandem Repeat Region ================================================ ttttctttcatagatatcaactattgaatttttatcaactgttcttgttgcactttcttctggaatatctttaacatcttctgtgtttttagcagtttctacacttttttcttttgttgcttttttttctgtttttcctcctactatttcattggaaatttggtcaagtgactcaacttcttttatttcagcactcaataaagaaaagttaaataatactcctgctaaaataaaaaacttagtaaatttgttcattgttttgttctccta Find is-nt database================================================ Query_seq: FN1230:FN1231|FN1230:FN1231:Hypothetical cytosolic protein:Inosine-5'-monophosphate dehydrogenase:<-<-:1887263..1887532 270 ttttctttcatagatatcaactattgaatttttatcaactgttcttgttgcactttcttctggaatatctttaacatcttctgtgtttttagcagtttctacacttttttcttttgttgcttttttttctgtttttcctcctactatttcattggaaatttggtcaagtgactcaacttcttttatttcagcactcaataaagaaaagttaaataatactcctgctaaaataaaaaacttagtaaatttgttcattgttttgttctccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1230:FN1231|FN1230:FN1231:Hypothetical cytosolic protein:Inosine-5'-monophosphate dehydrogenase:<-<-:1887263..1887532 270 ttttctttcatagatatcaactattgaatttttatcaactgttcttgttgcactttcttctggaatatctttaacatcttctgtgtttttagcagtttctacacttttttcttttgttgcttttttttctgtttttcctcctactatttcattggaaatttggtcaagtgactcaacttcttttatttcagcactcaataaagaaaagttaaataatactcctgctaaaataaaaaacttagtaaatttgttcattgttttgttctccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1230:FN1231|FN1230:FN1231:Hypothetical cytosolic protein:Inosine-5'-monophosphate dehydrogenase:<-<-:1887263..1887532 270 ttttctttcatagatatcaactattgaatttttatcaactgttcttgttgcactttcttctggaatatctttaacatcttctgtgtttttagcagtttctacacttttttcttttgttgcttttttttctgtttttcctcctactatttcattggaaatttggtcaagtgactcaacttcttttatttcagcactcaataaagaaaagttaaataatactcctgctaaaataaaaaacttagtaaatttgttcattgttttgttctccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttctttcatagatatcaactattgaatttttatcaactgttcttgttgcactttcttctggaatatctttaacatcttctgtgtttttagcagtttctacacttttttcttttgttgcttttttttctgtttttcctcctactatttcattggaaatttggtcaagtgactcaacttcttttatttcagcactcaataaagaaaagttaaataatactcctgctaaaataaaaaacttagtaaatttgttcattgttttgttctccta Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 28 End: 168 ........................... M F I N C S C C T F F W N I F N I F C V F S S F Y T F F F C C F F F C F S S Y Y F I G N L V K ...................................................................................................... Protein_Len: 32 Strand: + Start: 114 End: 209 ................................................................................................................. M L L F F L F F L L L F H W K F G Q V T Q L L L F Q H S I K K S ............................................................. Protein_Len: 60 Strand: + Start: 14 End: 268 ............. M S T I E F L S T V L V A L S S G I S L T S S V F L A V S T L F S F V A F F S V F P P T I S L E I W S S D S T S F I S A .. Protein_Len: 60 Strand: - Start: 1 End: 255 D E T N K A T E V S K E K T A K K E T K G G V I E N S I Q D L S E V E K I E A S L L S F N F L V G A L I F F K T F K N M ............... ttttctttcatagatatcaactattgaatttttatcaactgttcttgttgcactttcttctggaatatctttaacatcttctgtgtttttagcagtttctacacttttttcttttgttgcttttttttctgtttttcctcctactatttcattggaaatttggtcaagtgactcaacttcttttatttcagcactcaataaagaaaagttaaataatactcctgctaaaataaaaaacttagtaaatttgttcattgttttgttctccta 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================================================ ttttctttcatagatatcaactattgaatttttatcaactgttcttgttgcactttcttctggaatatctttaacatcttctgtgtttttagcagtttctacacttttttcttttgttgcttttttttctgtttttcctcctactatttcattggaaatttggtcaagtgactcaacttcttttatttcagcactcaataaagaaaagttaaataatactcctgctaaaataaaaaacttagtaaatttgttcattgttttgttctccta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1230:FN1231|FN1230:FN1231:Hypothetical cytosolic protein:Inosine-5'-monophosphate dehydrogenase:<-<-:1887263..1887532 270 ttttctttcatagatatcaactattgaatttttatcaactgttcttgttgcactttcttctggaatatctttaacatcttctgtgtttttagcagtttctacacttttttcttttgttgcttttttttctgtttttcctcctactatttcattggaaatttggtcaagtgactcaacttcttttatttcagcactcaataaagaaaagttaaataatactcctgctaaaataaaaaacttagtaaatttgttcattgttttgttctccta Intra-Species Hit: Count: 1 Min: 1 Max: 270 Len: 270 Subject: NC_003454_FN1230_FN1231|Hypothetical cytosolic protein:Inosine-5'-monophosphate dehydrogenase|NEGATIVE:NEGATIVE|[1887263,1887532]|270 HSP 1 e-value: 4.0E-70 bit: 266.0 Len: 134 Query Start:137 Query End:270 Subject Strand: POSITIVE Subject Start: 137 Subject End: 270 ........................................................................................................................................cctcctactatttcattggaaatttggtcaagtgactcaacttcttttatttcagcactcaataaagaaaagttaaataatactcctgctaaaataaaaaacttagtaaatttgttcattgttttgttctccta ........................................................................................................................................cctcctactatttcattggaaatttggtcaagtgactcaacttcttttatttcagcactcaataaagaaaagttaaataatactcctgctaaaataaaaaacttagtaaatttgttcattgttttgttctccta HSP 2 e-value: 6.0E-41 bit: 168.0 Len: 85 Query Start:1 Query End:85 Subject Strand: POSITIVE Subject Start: 1 Subject End: 85 ttttctttcatagatatcaactattgaatttttatcaactgttcttgttgcactttcttctggaatatctttaacatcttctgtg......................................................................................................................................................................................... ttttctttcatagatatcaactattgaatttttatcaactgttcttgttgcactttcttctggaatatctttaacatcttctgtg......................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUUCAUAGAUAUCAACUAUUGAAUUUUUAUCAACUGUUCUUGUUGCACUUUCUUCUGGAAUAUCUUUAACAUCUUCUGUGUUUUUAGCAGUUUCUACACUUUUUUCUUUUGUUGCUUUUUUUUCUGUUUUUCCUCCUACUAUUUCAUUGGAAAUUUGGUCAAGUGACUCAACUUCUUUUAUUUCAGCACUCAAUAAAGAAAAGUUAAAUAAUACUCCUGCUAAAAUAAAAAACUUAGUAAAUUUGUUCAUUGUUUUGUUCUCCUA ............((((..(((..((((.......))))..)))..)))).............(((((..((((.............(((((((((..........(((((((((((.((((............(((((...............))))).((((((....))).))).............))))..))..))))))))).............)))))))))............))))..)))))................. (-33.67) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGAGAACAAAACAAUGAACAAAUUUACUAAGUUUUUUAUUUUAGCAGGAGUAUUAUUUAACUUUUCUUUAUUGAGUGCUGAAAUAAAAGAAGUUGAGUCACUUGACCAAAUUUCCAAUGAAAUAGUAGGAGGAAAAACAGAAAAAAAAGCAACAAAAGAAAAAAGUGUAGAAACUGCUAAAAACACAGAAGAUGUUAAAGAUAUUCCAGAAGAAAGUGCAACAAGAACAGUUGAUAAAAAUUCAAUAGUUGAUAUCUAUGAAAGAAAA ..(((((((.....(((......)))......))))))).(((((((((......(((((...((((((((..((..((((.............(((.(((....)))))).(((((.((......)).)))))...............)))).)))))))))))))))......)))))))))...((..(((((((((...((((...(((.......((((.......)))).......))))))).))))))))).))........ (-41.44) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 778 100 51 191 142 NC_003454:FN1230|5end_Hypothetical_cytosolic_protein_1887172..1887402_NEGATIVE 328 100 51 163 94 NC_003454:FN1626|5end_LSU_ribosomal_protein_L30P_133049..133279_NEGATIVE 310 136 94 136 92 NC_003454:FN0577|5end_hypothetical_protein_1227237..1227467_POSITIVE 286 123 87 68 31 NC_003454:FN1988|5end_Tyrosine_phenol-lyase_490918..491148_POSITIVE 285 148 105 59 16 NC_003454:FN2032|5end_DNA-directed_RNA_polymerase_omega_chain_537315..537545_NEGATIVE 281 128 84 108 56 NC_003454:FN0602|5end_hypothetical_protein_1256649..1256879_POSITIVE 278 143 104 104 57 NC_003454:FN1223|5end_Dihydropteridine_reductase_1882511..1882741_NEGATIVE 277 138 92 70 33 NC_003454:FN1258|5end_C4-dicarboxylate-binding_protein_1914793..1915023_NEGATIVE 269 130 82 130 80 NC_003454:FN1895|5end_hypothetical_protein_382871..383101_NEGATIVE 268 121 83 190 141 NC_003454:FN1968|5end_Hemin_transport_system_ATP-binding_protein_hmuV_467189..467419_NEGATIVE 264 114 76 64 23 NC_003454:FN1028|5end_deoxyuridine_5'-triphosphate_nucleotidohydrolase_1682383..1682613_NEGATIVE 263 146 111 45 1 NC_003454:FN1432|5end_Leucine-,_isoleucine-,_valine-,_threonine-,_and_alanine-binding_protein_2101580..2101810_NEGATIVE 263 143 104 103 52 NC_003454:FN0896|5end_hypothetical_protein_1555780..1556010_NEGATIVE 255 143 102 208 168 NC_003454:FN1370|5end_Endonuclease_2019349..2019579_NEGATIVE 255 127 81 62 19 NC_003454:FN0090|5end_Ethanolamine_utilization_protein_eutQ_726315..726545_POSITIVE 255 122 86 69 30 NC_003454:FN2082|5end_Formate--tetrahydrofolate_ligase_594891..595121_NEGATIVE 253 140 92 221 167 NC_003454:FN1289|5end_hypothetical_protein_1946447..1946677_NEGATIVE 253 100 62 119 78 NC_003454:FN0728|5end_hypothetical_protein_1386120..1386350_NEGATIVE 253 138 92 231 182 NC_003454:FN0197|5end_Methyltransferase_822664..822894_POSITIVE 251 143 114 231 202 NC_003454:FN0088|5end_hypothetical_protein_724887..725117_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 100 51 150 81 NC_003454:FN1627|3end_SSU_ribosomal_protein_S5P_133062..133212_NEGATIVE 310 136 94 121 77 NC_003454:FN0576|3end_D-amino_acid_dehydrogenase_large_subunit_1227302..1227452_POSITIVE 278 143 104 75 28 NC_003454:FN1224|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1882540..1882690_NEGATIVE 269 130 82 114 64 NC_003454:FN1896|3end_ABC_transporter_integral_membrane_protein_382887..383037_NEGATIVE 264 114 76 62 21 NC_003454:FN1029|3end_Zinc_protease_1682385..1682535_NEGATIVE 258 70 24 126 74 NC_003454:FN1292|3end_hypothetical_protein_1949443..1949593_NEGATIVE 255 127 81 51 8 NC_003454:FN0089|3end_Ethanolamine_permease_726384..726534_POSITIVE 251 147 104 83 35 NC_003454:FN1319|3end_DNA_primase_1972386..1972536_NEGATIVE 250 72 40 60 17 NC_003454:FN0742|3end_hypothetical_protein_1400671..1400821_POSITIVE 247 100 53 145 100 NC_003454:FN1441|3end_PTS_system,_fructose-specific_IIABC_component_2110123..2110273_POSITIVE 242 99 54 147 113 NC_003454:FN0926|3end_GTP_pyrophosphokinase_1581671..1581821_POSITIVE 239 226 186 59 22 NC_003454:FN0723|3end_hypothetical_protein_1383464..1383614_POSITIVE 239 89 47 68 27 NC_003454:FN1639|3end_SSU_ribosomal_protein_S3P_137504..137654_NEGATIVE 238 167 133 117 78 NC_003454:FN0309|3end_Iron(III)-transport_system_permease_protein_sfuB_945861..946011_POSITIVE 234 129 81 92 40 NC_003454:FN0546|3end_Lipopolysaccharide_core_biosynthesis_protein_rfaQ_1199726..1199876_POSITIVE 233 87 41 119 69 NC_003454:FN1994|3end_hypothetical_protein_498091..498241_POSITIVE 231 153 111 141 102 NC_003454:FN1472|3end_N-acetylneuraminate-binding_protein_2155088..2155238_POSITIVE 231 190 141 115 66 NC_003454:FN0651|3end_Ribosomal_large_subunit_pseudouridine_synthase_D_1310260..1310410_POSITIVE 231 98 51 146 92 NC_003454:FN0605|3end_aspartate_aminotransferase_1261097..1261247_POSITIVE 230 125 81 143 99 NC_003454:FN0733|3end_peptidase_T_1390882..1391032_POSITIVE