Origin IGS: actgtaaaaatgaactgcgccttcaatcttgtatcaaagattttgggtgtagtttattttaataagttattatacactaaataaatcataattagttattttatataatatttgtatttgttgtgtgtctattttttggtacaatgtttaagattatataaatattttattaggagagaatttt .........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 aaaattctctcctaataaaatatttatataatcttaaacattgtaccaaaaaatagacacacaacaaatacaaatattatataaaataactaattatgatttatttagtgtataataacttattaaaataaactacacccaaaatctttgatacaagattgaaggcgcagttcatttttacagt Mask Tandem Repeat Region ================================================ actgtaaaaatgaactgcgccttcaatcttgtatcaaagattttgggtgtagtttattttaataagttattatacactaaataaatcataattagttattttatataatatttgtatttgttgtgtgtctattttttggtacaatgtttaagattatataaatattttattaggagagaatttt Find is-nt database================================================ Query_seq: FN1498:FN1499|FN1498:FN1499:Integral membrane protein:Cell surface protein:->->:3603..3786 184 actgtaaaaatgaactgcgccttcaatcttgtatcaaagattttgggtgtagtttattttaataagttattatacactaaataaatcataattagttattttatataatatttgtatttgttgtgtgtctattttttggtacaatgtttaagattatataaatattttattaggagagaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1498:FN1499|FN1498:FN1499:Integral membrane protein:Cell surface protein:->->:3603..3786 184 actgtaaaaatgaactgcgccttcaatcttgtatcaaagattttgggtgtagtttattttaataagttattatacactaaataaatcataattagttattttatataatatttgtatttgttgtgtgtctattttttggtacaatgtttaagattatataaatattttattaggagagaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1498:FN1499|FN1498:FN1499:Integral membrane protein:Cell surface protein:->->:3603..3786 184 actgtaaaaatgaactgcgccttcaatcttgtatcaaagattttgggtgtagtttattttaataagttattatacactaaataaatcataattagttattttatataatatttgtatttgttgtgtgtctattttttggtacaatgtttaagattatataaatattttattaggagagaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actgtaaaaatgaactgcgccttcaatcttgtatcaaagattttgggtgtagtttattttaataagttattatacactaaataaatcataattagttattttatataatatttgtatttgttgtgtgtctattttttggtacaatgtttaagattatataaatattttattaggagagaatttt Predict ORF larger than 30AA ================================================ actgtaaaaatgaactgcgccttcaatcttgtatcaaagattttgggtgtagtttattttaataagttattatacactaaataaatcataattagttattttatataatatttgtatttgttgtgtgtctattttttggtacaatgtttaagattatataaatattttattaggagagaatttt 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================================================ actgtaaaaatgaactgcgccttcaatcttgtatcaaagattttgggtgtagtttattttaataagttattatacactaaataaatcataattagttattttatataatatttgtatttgttgtgtgtctattttttggtacaatgtttaagattatataaatattttattaggagagaatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1498:FN1499|FN1498:FN1499:Integral membrane protein:Cell surface protein:->->:3603..3786 184 actgtaaaaatgaactgcgccttcaatcttgtatcaaagattttgggtgtagtttattttaataagttattatacactaaataaatcataattagttattttatataatatttgtatttgttgtgtgtctattttttggtacaatgtttaagattatataaatattttattaggagagaatttt Intra-Species Hit: Count: 1 Min: 1 Max: 184 Len: 184 Subject: NC_003454_FN1498_FN1499|Integral membrane protein:Cell surface protein|POSITIVE:POSITIVE|[3603,3786]|184 HSP 1 e-value: 1.0E-100 bit: 365.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 actgtaaaaatgaactgcgccttcaatcttgtatcaaagattttgggtgtagtttattttaataagttattatacactaaataaatcataattagttattttatataatatttgtatttgttgtgtgtctattttttggtacaatgtttaagattatataaatattttattaggagagaatttt actgtaaaaatgaactgcgccttcaatcttgtatcaaagattttgggtgtagtttattttaataagttattatacactaaataaatcataattagttattttatataatatttgtatttgttgtgtgtctattttttggtacaatgtttaagattatataaatattttattaggagagaatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGUAAAAAUGAACUGCGCCUUCAAUCUUGUAUCAAAGAUUUUGGGUGUAGUUUAUUUUAAUAAGUUAUUAUACACUAAAUAAAUCAUAAUUAGUUAUUUUAUAUAAUAUUUGUAUUUGUUGUGUGUCUAUUUUUUGGUACAAUGUUUAAGAUUAUAUAAAUAUUUUAUUAGGAGAGAAUUUU ..(((.((((((((((((((((..((((((......))))))..)))))))))))))))).))).......((((((..(((((((.((((...(((((.....)))))..)))))))))))))))))...((((((((((.((((((((........)))))))).))))))))))....... (-45.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUCUCUCCUAAUAAAAUAUUUAUAUAAUCUUAAACAUUGUACCAAAAAAUAGACACACAACAAAUACAAAUAUUAUAUAAAAUAACUAAUUAUGAUUUAUUUAGUGUAUAAUAACUUAUUAAAAUAAACUACACCCAAAAUCUUUGAUACAAGAUUGAAGGCGCAGUUCAUUUUUACAGU .......................................((((((.............................(((((((((...(((.(((.......))).))).))))))))).......(((((.((((.(.((...((((((......))))))...)).).)))).))))))))))) (-18.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 554 59 11 143 91 NC_003454:FN0786|5end_Transposase_1442465..1442695_POSITIVE 540 57 13 226 178 NC_003454:FN1972|5end_hypothetical_protein_472071..472301_NEGATIVE 537 57 13 128 80 NC_003454:FN1446|5end_Transposase_2116033..2116263_POSITIVE 535 57 13 139 90 NC_003454:FN0840|5end_Transposase_1501361..1501591_POSITIVE 524 56 13 139 92 NC_003454:FN1887|5end_Transposase_371671..371901_POSITIVE 523 56 11 140 91 NC_003454:FN1443|5end_Transposase_2111518..2111748_NEGATIVE 523 56 11 140 91 NC_003454:FN0135|5end_Transposase_770238..770468_POSITIVE 522 56 13 138 90 NC_003454:FN0485|5end_Transposase_1130267..1130497_POSITIVE 396 55 11 210 167 NC_003454:FN0210|5end_Transcriptional_regulator,_COPG_family_836998..837228_POSITIVE 384 32 2 228 197 NC_003454:FN0234|5end_hypothetical_protein_859499..859729_NEGATIVE 377 55 11 203 159 NC_003454:FN1444|5end_GMP_synthase_[glutamine-hydrolyzing]_2111585..2111815_POSITIVE 377 55 11 73 29 NC_003454:FN0839|5end_hypothetical_protein_1501426..1501656_NEGATIVE 232 50 1 187 142 NC_003454:FN1977|5end_Cell_cycle_protein_MesJ_478136..478366_POSITIVE 230 54 11 203 159 NC_003454:FN0288|5end_Hypoxanthine-guanine_phosphoribosyltransferase_915765..915995_NEGATIVE 208 168 124 174 124 NC_003454:FN1538|5end_Arsenical_pump-driving_ATPase_52299..52529_NEGATIVE 201 143 107 219 186 NC_003454:FN0792|5end_urocanate_hydratase_1448263..1448493_POSITIVE 201 156 121 170 136 NC_003454:FN1645|5end_LSU_ribosomal_protein_L3P_141301..141531_NEGATIVE 186 53 15 110 75 NC_003454:FN0068|5end_Lipoprotein_signal_peptidase_707308..707538_POSITIVE 185 56 13 171 137 NC_003454:FN1464|5end_1-deoxy-D-xylulose-5-phosphate_synthase_2147705..2147935_NEGATIVE 185 48 2 105 58 NC_003454:FN1186|5end_Amidohydrolase_1848756..1848986_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 623 56 11 77 32 NC_003454:FN0235|3end_ABC_transporter_ATP-binding_protein_859674..859824_NEGATIVE 540 57 13 67 19 NC_003454:FN1973|3end_Translation_initiation_inhibitor_472230..472380_NEGATIVE 534 54 12 81 39 NC_003454:FN1464|3end_1-deoxy-D-xylulose-5-phosphate_synthase_2145954..2146104_NEGATIVE 534 60 11 90 39 NC_003454:FN1905|3end_168_kDa_surface-layer_protein_precursor_393653..393803_NEGATIVE 524 56 13 142 95 NC_003454:FN1886|3end_hypothetical_protein_371754..371904_POSITIVE 522 56 13 63 15 NC_003454:FN0484|3end_Lipase_1130272..1130422_POSITIVE 510 53 11 75 28 NC_003454:FN1547|3end_PTS_permease_for_N-acetylglucosamine_and_glucose_61801..61951_NEGATIVE 476 59 11 92 43 NC_003454:FN1500|3end_Nickel_transport_ATP-binding_protein_nikE_5193..5343_NEGATIVE 414 53 11 80 38 NC_003454:FN1221|3end_hypothetical_protein_1881290..1881440_POSITIVE 410 60 11 92 41 NC_003454:FN1545|3end_Ferredoxin_like_protein_59497..59647_POSITIVE 359 53 11 43 1 NC_003454:FN1019|3end_3-hydroxybutyryl-CoA_dehydrogenase_1672945..1673095_NEGATIVE 356 60 11 83 32 NC_003454:FN1546|3end_translation_elongation_factor_EF-G_59529..59679_NEGATIVE 351 54 12 82 40 NC_003454:FN1463|3end_pyridoxine_biosynthesis_protein_2145924..2146074_POSITIVE 350 55 14 72 38 NC_003454:FN0435|3end_Purine_nucleoside_phosphorylase_1077821..1077971_POSITIVE 335 60 11 77 24 NC_003454:FN1144|3end_hypothetical_protein_1793403..1793553_NEGATIVE 335 60 11 97 46 NC_003454:FN1904|3end_Transcriptional_regulator,_MarR_family_393633..393783_POSITIVE 332 60 11 84 35 NC_003454:FN1498|3end_Integral_membrane_protein_3542..3692_POSITIVE 284 55 11 71 23 NC_003454:FN0178|3end_UNC-44_ankyrins_802390..802540_NEGATIVE 280 55 11 85 41 NC_003454:FN1143|3end_glucosamine-6-phosphate_deaminase_1793365..1793515_POSITIVE 280 60 13 97 48 NC_003454:FN1720|3end_hypothetical_protein_218771..218921_NEGATIVE