Origin IGS: tttgccctcctatctactgttactgaaaataagattaaatatagattaagactgctgcgacgtccattattatttcaagagcctcgcggagctcttgaaataataatagcaggcaagcagtcgttataaataa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttatttataacgactgcttgcctgctattattatttcaagagctccgcgaggctcttgaaataataatggacgtcgcagcagtcttaatctatatttaatcttattttcagtaacagtagataggagggcaaa Mask Tandem Repeat Region ================================================ tttgccctcctatctactgttactgaaaataagattaaatatagattaagactgctgcgacgtccattattatttcaagagcctcgcggagctcttgaaataataatagcaggcaagcagtcgttataaataa Find is-nt database================================================ Query_seq: FN1351:FN1352|FN1351:FN1352:15 kDa lipoprotein precursor:ABC transporter ATP-binding protein:<-<-:2003463..2003595 133 tttgccctcctatctactgttactgaaaataagattaaatatagattaagactgctgcgacgtccattattatttcaagagcctcgcggagctcttgaaataataatagcaggcaagcagtcgttataaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1351:FN1352|FN1351:FN1352:15 kDa lipoprotein precursor:ABC transporter ATP-binding protein:<-<-:2003463..2003595 133 tttgccctcctatctactgttactgaaaataagattaaatatagattaagactgctgcgacgtccattattatttcaagagcctcgcggagctcttgaaataataatagcaggcaagcagtcgttataaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1351:FN1352|FN1351:FN1352:15 kDa lipoprotein precursor:ABC transporter ATP-binding protein:<-<-:2003463..2003595 133 tttgccctcctatctactgttactgaaaataagattaaatatagattaagactgctgcgacgtccattattatttcaagagcctcgcggagctcttgaaataataatagcaggcaagcagtcgttataaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgccctcctatctactgttactgaaaataagattaaatatagattaagactgctgcgacgtccattattatttcaagagcctcgcggagctcttgaaataataatagcaggcaagcagtcgttataaataa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 34 End: 126 ................................. M K Y R L R L L R R P L L F Q E P R G A L E I I I A G K Q S L ....... Protein_Len: 30 Strand: - Start: 38 End: 127 ..................................... I Y I L V A A V D M I I E L A E R L E Q F L L L L C A T T M ...... tttgccctcctatctactgttactgaaaataagattaaatatagattaagactgctgcgacgtccattattatttcaagagcctcgcggagctcttgaaataataatagcaggcaagcagtcgttataaataa 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================================================ tttgccctcctatctactgttactgaaaataagattaaatatagattaagactgctgcgacgtccattattatttcaagagcctcgcggagctcttgaaataataatagcaggcaagcagtcgttataaataa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1351:FN1352|FN1351:FN1352:15 kDa lipoprotein precursor:ABC transporter ATP-binding protein:<-<-:2003463..2003595 133 tttgccctcctatctactgttactgaaaataagattaaatatagattaagactgctgcgacgtccattattatttcaagagcctcgcggagctcttgaaataataatagcaggcaagcagtcgttataaataa Intra-Species Hit: Count: 1 Min: 1 Max: 133 Len: 133 Subject: NC_003454_FN1351_FN1352|15 kDa lipoprotein precursor:ABC transporter ATP-binding protein|NEGATIVE:NEGATIVE|[2003463,2003595]|133 HSP 1 e-value: 7.0E-70 bit: 264.0 Len: 133 Query Start:1 Query End:133 Subject Strand: POSITIVE Subject Start: 1 Subject End: 133 tttgccctcctatctactgttactgaaaataagattaaatatagattaagactgctgcgacgtccattattatttcaagagcctcgcggagctcttgaaataataatagcaggcaagcagtcgttataaataa tttgccctcctatctactgttactgaaaataagattaaatatagattaagactgctgcgacgtccattattatttcaagagcctcgcggagctcttgaaataataatagcaggcaagcagtcgttataaataa HSP 2 e-value: 5.0E-6 bit: 52.0 Len: 42 Query Start:66 Query End:107 Subject Strand: NEGATIVE Subject Start: 66 Subject End: 107 .................................................................attattatttcaagagcctcgcggagctcttgaaataataat.......................... .................................................................attattatttcaagagctccgcgaggctcttgaaataataat.......................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGCCCUCCUAUCUACUGUUACUGAAAAUAAGAUUAAAUAUAGAUUAAGACUGCUGCGACGUCCAUUAUUAUUUCAAGAGCCUCGCGGAGCUCUUGAAAUAAUAAUAGCAGGCAAGCAGUCGUUAUAAAUAA ...........(((((.((((.((.......))....)))))))))...(((((((((...((..((((((((((((((((((.....).))))))))))))))))).))..)).)))))))........... (-36.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUUAUAACGACUGCUUGCCUGCUAUUAUUAUUUCAAGAGCUCCGCGAGGCUCUUGAAAUAAUAAUGGACGUCGCAGCAGUCUUAAUCUAUAUUUAAUCUUAUUUUCAGUAACAGUAGAUAGGAGGGCAAA ...........(((((((.((.((((((((((((((((((((((......)))))))))))))))))))).))..)))))))))...............((((((((.(.......).))))))))....... (-45.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 979 100 51 191 142 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 537 100 52 212 164 NC_003454:FN1142|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1791529..1791759_POSITIVE 504 100 52 218 170 NC_003454:FN1740|5end_ATP_synthase_subunit_K_238400..238630_NEGATIVE 492 100 51 219 169 NC_003454:FN0054|5end_tyrosyl-tRNA_synthetase_690836..691066_POSITIVE 465 100 52 192 144 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 465 100 52 88 40 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 415 100 51 221 172 NC_003454:FN1581|5end_DNA_mismatch_repair_protein_mutS_93231..93461_NEGATIVE 392 100 53 226 180 NC_003454:FN1328|5end_Exodeoxyribonuclease_VII_small_subunit_1983129..1983359_NEGATIVE 359 100 53 202 157 NC_003454:FN1995|5end_hypothetical_protein_498245..498475_POSITIVE 327 82 47 206 172 NC_003454:FN0220|5end_Autolysin_sensor_kinase_844934..845164_NEGATIVE 304 97 55 45 1 NC_003454:FN1544|5end_Probable_electron_transfer_flavoprotein-quinone_oxidoreductase_ydiS_57835..58065_POSITIVE 295 97 56 209 150 NC_003454:FN1935|5end_Adenine-specific_methyltransferase_437061..437291_NEGATIVE 250 87 41 54 10 NC_003454:FN1192|5end_hypothetical_protein_1854679..1854909_POSITIVE 248 39 5 127 93 NC_003454:FN0449|5end_hypothetical_protein_1092683..1092913_POSITIVE 243 82 42 224 185 NC_003454:FN1731|5end_Anthranilate_synthase_component_II_231037..231267_NEGATIVE 238 114 71 70 23 NC_003454:FN1498|5end_Integral_membrane_protein_2563..2793_POSITIVE 234 100 51 66 3 NC_003454:FN1736|5end_V-type_sodium_ATP_synthase_subunit_A_236021..236251_NEGATIVE 233 99 52 158 115 NC_003454:FN1699|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_194851..195081_NEGATIVE 231 96 52 72 35 NC_003454:FN2046|5end_Acetyltransferase_551360..551590_NEGATIVE 225 41 1 90 53 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 504 100 52 57 9 NC_003454:FN1741|3end_ATP_synthase_subunit_I_238561..238711_NEGATIVE 392 100 51 58 9 NC_003454:FN0828|3end_ABC_transporter_permease_protein_1489505..1489655_POSITIVE 316 120 79 65 23 NC_003454:FN1259|3end_Uracil-DNA_glycosylase_1915756..1915906_POSITIVE 295 97 56 128 69 NC_003454:FN1936|3end_hypothetical_protein_437142..437292_NEGATIVE 248 39 5 111 77 NC_003454:FN0448|3end_DNA-repair_protein_1092747..1092897_POSITIVE 223 119 73 81 33 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 221 125 86 48 3 NC_003454:FN0655|3end_hypothetical_protein_1313790..1313940_POSITIVE 221 97 56 51 9 NC_003454:FN0005|3end_Jag_protein_644579..644729_POSITIVE 220 60 13 62 16 NC_003454:FN1140|3end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_1790473..1790623_POSITIVE 220 99 53 124 59 NC_003454:FN0272|3end_Acetoacetate:butyrate/acetate_coenzyme_A_transferase_899503..899653_POSITIVE 217 90 47 66 24 NC_003454:FN0718|3end_hypothetical_protein_1376004..1376154_POSITIVE 209 96 67 148 111 NC_003454:FN1505|3end_6,7-dimethyl-8-ribityllumazine_synthase_10949..11099_POSITIVE 207 120 73 64 19 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 198 106 62 101 55 NC_003454:FN0013|3end_Transporter_652639..652789_POSITIVE 195 97 51 129 87 NC_003454:FN0132|3end_Hemolysin_769183..769333_POSITIVE 195 120 73 81 38 NC_003454:FN2092|3end_Integral_membrane_protein_602614..602764_NEGATIVE 192 122 86 62 18 NC_003454:FN1267|3end_hypothetical_protein_1923054..1923204_NEGATIVE 192 111 71 51 6 NC_003454:FN1162|3end_Hydroxyacylglutathione_hydrolase_1820864..1821014_POSITIVE 188 118 73 134 89 NC_003454:FN0771|3end_Oxygen-independent_coproporphyrinogen_III_oxidase_1428777..1428927_POSITIVE 188 96 60 135 93 NC_003454:FN0675|3end_60_kDa_chaperonin_GROEL_1330471..1330621_NEGATIVE