Origin IGS: ttttttctactccttctactatcttctgttctacctaatattagattaaaaaaataaacgaattacgaatgtagattttttatcgttaagaaatctactcagtaatgagttattttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaataactcattactgagtagatttcttaacgataaaaaatctacattcgtaattcgtttatttttttaatctaatattaggtagaacagaagatagtagaaggagtagaaaaaa Mask Tandem Repeat Region ================================================ ttttttctactccttctactatcttctgttctacctaatattagattaaaaaaataaacgaattacgaatgtagattttttatcgttaagaaatctactcagtaatgagttattttt Find is-nt database================================================ Query_seq: FN2080:FN2081|FN2080:FN2081:ABC transporter integral membrane protein:ABC transporter substrate-binding protein:<-<-:592048..592164 117 ttttttctactccttctactatcttctgttctacctaatattagattaaaaaaataaacgaattacgaatgtagattttttatcgttaagaaatctactcagtaatgagttattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2080:FN2081|FN2080:FN2081:ABC transporter integral membrane protein:ABC transporter substrate-binding protein:<-<-:592048..592164 117 ttttttctactccttctactatcttctgttctacctaatattagattaaaaaaataaacgaattacgaatgtagattttttatcgttaagaaatctactcagtaatgagttattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2080:FN2081|FN2080:FN2081:ABC transporter integral membrane protein:ABC transporter substrate-binding protein:<-<-:592048..592164 117 ttttttctactccttctactatcttctgttctacctaatattagattaaaaaaataaacgaattacgaatgtagattttttatcgttaagaaatctactcagtaatgagttattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttttctactccttctactatcttctgttctacctaatattagattaaaaaaataaacgaattacgaatgtagattttttatcgttaagaaatctactcagtaatgagttattttt Predict ORF larger than 30AA ================================================ ttttttctactccttctactatcttctgttctacctaatattagattaaaaaaataaacgaattacgaatgtagattttttatcgttaagaaatctactcagtaatgagttattttt 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================================================ ttttttctactccttctactatcttctgttctacctaatattagattaaaaaaataaacgaattacgaatgtagattttttatcgttaagaaatctactcagtaatgagttattttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN2080:FN2081|FN2080:FN2081:ABC transporter integral membrane protein:ABC transporter substrate-binding protein:<-<-:592048..592164 117 ttttttctactccttctactatcttctgttctacctaatattagattaaaaaaataaacgaattacgaatgtagattttttatcgttaagaaatctactcagtaatgagttattttt Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_003454_FN2080_FN2081|ABC transporter integral membrane protein:ABC transporter substrate-binding protein|NEGATIVE:NEGATIVE|[592048,592164]|117 HSP 1 e-value: 7.0E-48 bit: 190.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 ttttttctactccttctactatcttctgttctacctaatattagattnnnnnnntaaacgaattacgaatgtagattttttatcgttaagaaatctactcagtaatgagttattttt ttttttctactccttctactatcttctgttctacctaatattagattaaaaaaataaacgaattacgaatgtagattttttatcgttaagaaatctactcagtaatgagttattttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUCUACUCCUUCUACUAUCUUCUGUUCUACCUAAUAUUAGAUUAAAAAAAUAAACGAAUUACGAAUGUAGAUUUUUUAUCGUUAAGAAAUCUACUCAGUAAUGAGUUAUUUUU ....................((((..((((......))))..))))...((((((((.(..(((((....((((((((((((....))))))))))))...)))))..))))))))) (-21.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUAACUCAUUACUGAGUAGAUUUCUUAACGAUAAAAAAUCUACAUUCGUAAUUCGUUUAUUUUUUUAAUCUAAUAUUAGGUAGAACAGAAGAUAGUAGAAGGAGUAGAAAAAA .......((((..(((.((((((((((.(((....))).)))))))).)).))).(((..(((((((((...((((........))))..)))))))))..))).))))........ (-19.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 724 50 1 141 92 NC_003454:FN2080|5end_ABC_transporter_integral_membrane_protein_591957..592187_NEGATIVE 508 110 67 197 154 NC_003454:FN0921|5end_hypothetical_protein_1576482..1576712_NEGATIVE 456 110 66 93 48 NC_003454:FN0171|5end_Hypothetical_cytosolic_protein_796548..796778_POSITIVE 453 100 51 226 181 NC_003454:FN1350|5end_Integral_membrane_protein_2002796..2003026_NEGATIVE 400 108 63 203 162 NC_003454:FN0423|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit_1066328..1066558_POSITIVE 370 108 61 231 188 NC_003454:FN1347|5end_Hypothetical_cytosolic_protein_2000300..2000530_NEGATIVE 322 108 66 94 51 NC_003454:FN0797|5end_hypothetical_protein_1455799..1456029_NEGATIVE 293 47 1 75 22 NC_003454:FN1734|5end_V-type_ATP_synthase_subunit_B_234258..234488_NEGATIVE 280 108 66 163 109 NC_003454:FN1821|5end_Hypothetical_cytosolic_protein_311031..311261_POSITIVE 256 36 4 111 81 NC_003454:FN0084|5end_Acetaldehyde_dehydrogenase_[acetylating]_721572..721802_POSITIVE 235 42 8 141 99 NC_003454:FN1214|5end_Fe-S_oxidoreductase_1875473..1875703_NEGATIVE 232 70 29 135 94 NC_003454:FN0072|5end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_711715..711945_POSITIVE 227 49 1 115 60 NC_003454:FN0325|5end_50S_ribosomal_protein_L20_961274..961504_NEGATIVE 211 42 1 86 45 NC_003454:FN1609|5end_hypothetical_protein_119613..119843_NEGATIVE 210 36 11 123 97 NC_003454:FN1032|5end_hypothetical_protein_1686348..1686578_NEGATIVE 208 33 1 120 83 NC_003454:FN1336|5end_hypothetical_protein_1990304..1990534_NEGATIVE 204 42 13 197 165 NC_003454:FN1829|5end_hypothetical_protein_318556..318786_NEGATIVE 201 32 10 46 25 NC_003454:FN1319|5end_DNA_primase_1974197..1974427_NEGATIVE 198 32 1 109 73 NC_003454:FN1105|5end_hypothetical_protein_1750041..1750271_POSITIVE 198 37 7 224 197 NC_003454:FN0118|5end_Chaperone_protein_dnaJ_750898..751128_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 508 110 67 91 48 NC_003454:FN0922|3end_Homoserine_kinase_1576588..1576738_NEGATIVE 491 110 61 82 37 NC_003454:FN1351|3end_15_kDa_lipoprotein_precursor_2002950..2003100_NEGATIVE 456 110 66 78 33 NC_003454:FN0170|3end_GTP-binding_protein_796613..796763_POSITIVE 400 108 63 78 37 NC_003454:FN0422|3end_carbamoyl-phosphate_synthase_large_subunit_1066283..1066433_POSITIVE 370 108 61 61 18 NC_003454:FN1348|3end_ABC_transporter_ATP-binding_protein_2000470..2000620_NEGATIVE 335 108 66 86 44 NC_003454:FN2005|3end_Cobalt_transport_ATP-binding_protein_cbiO_505976..506126_POSITIVE 323 110 66 73 28 NC_003454:FN0989|3end_phosphoribosylaminoimidazole_carboxylase_catalytic_subunit_1641194..1641344_NEGATIVE 298 109 66 84 29 NC_003454:FN1809|3end_Iron/zinc/copper-binding_protein_290180..290330_NEGATIVE 293 47 1 82 29 NC_003454:FN1735|3end_V-type_ATP_synthase_subunit_A_234251..234401_NEGATIVE 290 108 66 44 1 NC_003454:FN1826|3end_Protease_314654..314804_NEGATIVE 280 108 66 68 14 NC_003454:FN1820|3end_Export_ABC_transporter_311016..311166_POSITIVE 275 108 66 73 19 NC_003454:FN1461|3end_Histidinol-phosphatase_2141603..2141753_NEGATIVE 268 109 66 76 32 NC_003454:FN1487|3end_hypothetical_protein_2169559..2169709_NEGATIVE 267 36 1 130 97 NC_003454:FN1098|3end_hypothetical_protein_1743898..1744048_POSITIVE 265 108 66 73 30 NC_003454:FN1836|3end_Tetratricopeptide_repeat_family_protein_323904..324054_NEGATIVE 251 108 67 83 30 NC_003454:FN0391|3end_Hydrolase_(HAD_superfamily)_1029496..1029646_POSITIVE 251 108 74 69 35 NC_003454:FN0069|3end_glycyl-tRNA_synthetase_alpha_subunit_708761..708911_POSITIVE 250 109 66 76 21 NC_003454:FN0483|3end_Uracil_phosphoribosyltransferase_1129301..1129451_POSITIVE 241 108 66 45 3 NC_003454:FN0046|3end_3-dehydroquinate_dehydratase_684265..684415_POSITIVE 228 108 67 71 30 NC_003454:FN1218|3end_hypothetical_protein_1877812..1877962_NEGATIVE