Origin IGS: ttttaacctccatcaaataatatattggttgatacaacttacccttgtggttctattttttgacacaagaataaaatcaacttgtactattctgtaagtatgatgttttccaacatcatctcccataaataaatacaaagaatagaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttctattctttgtatttatttatgggagatgatgttggaaaacatcatacttacagaatagtacaagttgattttattcttgtgtcaaaaaatagaaccacaagggtaagttgtatcaaccaatatattatttgatggaggttaaaa Mask Tandem Repeat Region ================================================ ttttaacctccatcaaataatatattggttgatacaacttacccttgtggttctattttttgacacaagaataaaatcaacttgtactattctgtaagtatgatgttttccaacatcatctcccataaataaatacaaagaatagaa Find is-nt database================================================ Query_seq: FN1645:FN1646|FN1645:FN1646:LSU ribosomal protein L3P:SSU ribosomal protein S10P:<-<-:141392..141538 147 ttttaacctccatcaaataatatattggttgatacaacttacccttgtggttctattttttgacacaagaataaaatcaacttgtactattctgtaagtatgatgttttccaacatcatctcccataaataaatacaaagaatagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1645:FN1646|FN1645:FN1646:LSU ribosomal protein L3P:SSU ribosomal protein S10P:<-<-:141392..141538 147 ttttaacctccatcaaataatatattggttgatacaacttacccttgtggttctattttttgacacaagaataaaatcaacttgtactattctgtaagtatgatgttttccaacatcatctcccataaataaatacaaagaatagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1645:FN1646|FN1645:FN1646:LSU ribosomal protein L3P:SSU ribosomal protein S10P:<-<-:141392..141538 147 ttttaacctccatcaaataatatattggttgatacaacttacccttgtggttctattttttgacacaagaataaaatcaacttgtactattctgtaagtatgatgttttccaacatcatctcccataaataaatacaaagaatagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttaacctccatcaaataatatattggttgatacaacttacccttgtggttctattttttgacacaagaataaaatcaacttgtactattctgtaagtatgatgttttccaacatcatctcccataaataaatacaaagaatagaa Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 16 End: 138 ............... I I Y Q N I C S V R T T R N K S V L I F D V Q V I R Y T H H K G V D D G M F L Y M ......... ttttaacctccatcaaataatatattggttgatacaacttacccttgtggttctattttttgacacaagaataaaatcaacttgtactattctgtaagtatgatgttttccaacatcatctcccataaataaatacaaagaatagaa 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: 81 Start: 59 End: 88 ..........................................................TTTGACACAAGAATAAAATCAACTTGTACT........................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttaacctccatcaaataatatattggttgatacaacttacccttgtggttctattttttgacacaagaataaaatcaacttgtactattctgtaagtatgatgttttccaacatcatctcccataaataaatacaaagaatagaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1645:FN1646|FN1645:FN1646:LSU ribosomal protein L3P:SSU ribosomal protein S10P:<-<-:141392..141538 147 ttttaacctccatcaaataatatattggttgatacaacttacccttgtggttctattttttgacacaagaataaaatcaacttgtactattctgtaagtatgatgttttccaacatcatctcccataaataaatacaaagaatagaa Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: NC_003454_FN1645_FN1646|LSU ribosomal protein L3P:SSU ribosomal protein S10P|NEGATIVE:NEGATIVE|[141392,141538]|147 HSP 1 e-value: 3.0E-78 bit: 291.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 ttttaacctccatcaaataatatattggttgatacaacttacccttgtggttctattttttgacacaagaataaaatcaacttgtactattctgtaagtatgatgttttccaacatcatctcccataaataaatacaaagaatagaa ttttaacctccatcaaataatatattggttgatacaacttacccttgtggttctattttttgacacaagaataaaatcaacttgtactattctgtaagtatgatgttttccaacatcatctcccataaataaatacaaagaatagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAACCUCCAUCAAAUAAUAUAUUGGUUGAUACAACUUACCCUUGUGGUUCUAUUUUUUGACACAAGAAUAAAAUCAACUUGUACUAUUCUGUAAGUAUGAUGUUUUCCAACAUCAUCUCCCAUAAAUAAAUACAAAGAAUAGAA ..((((((..................))))))..........((....)).(((((((((((..(((((...........))))).......((..((.((((((((....))))))))))..))..........))))))))))). (-26.67) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUAUUCUUUGUAUUUAUUUAUGGGAGAUGAUGUUGGAAAACAUCAUACUUACAGAAUAGUACAAGUUGAUUUUAUUCUUGUGUCAAAAAAUAGAACCACAAGGGUAAGUUGUAUCAACCAAUAUAUUAUUUGAUGGAGGUUAAAA (((((((..(((((((.((((.((..((((((((((....)))))))).))..)))))))))))))((((((((((((((((((((........))..))))))))))))....)))))).............)))))))....... (-38.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 787 130 81 221 172 NC_003454:FN1645|5end_LSU_ribosomal_protein_L3P_141301..141531_NEGATIVE 240 63 21 171 127 NC_003454:FN0611|5end_Threonyl-tRNA_synthetase_1268359..1268589_POSITIVE 216 128 90 75 35 NC_003454:FN1254|5end_Dihydropteridine_reductase_1911014..1911244_NEGATIVE 213 126 81 107 68 NC_003454:FN1584|5end_Beta-lactamase_96158..96388_NEGATIVE 208 50 7 206 152 NC_003454:FN0445|5end_hypothetical_protein_1084816..1085046_POSITIVE 206 128 85 87 40 NC_003454:FN1354|5end_ABC_transporter_permease_protein_2006682..2006912_NEGATIVE 206 137 97 83 44 NC_003454:FN0206|5end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_832758..832988_POSITIVE 205 125 84 62 15 NC_003454:FN0176|5end_Cell_division_inhibitor_MinD_801157..801387_POSITIVE 204 127 109 68 44 NC_003454:FN0226|5end_4-hydroxythreonine-4-phosphate_dehydrogenase_854089..854319_NEGATIVE 198 66 24 222 160 NC_003454:FN1314|5end_hypothetical_protein_1968682..1968912_NEGATIVE 198 69 26 120 80 NC_003454:FN1751|5end_Pyruvate-flavodoxin_oxidoreductase_248067..248297_POSITIVE 194 123 87 226 192 NC_003454:FN1423|5end_Flavoprotein_2090070..2090300_NEGATIVE 193 122 81 181 129 NC_003454:FN0581|5end_Lipoprotein_releasing_system_transmembrane_protein_lolE_1237108..1237338_POSITIVE 192 127 92 229 201 NC_003454:FN1026|5end_tRNA_pseudouridine_synthase_A_1680823..1681053_NEGATIVE 188 126 90 155 120 NC_003454:FN1363|5end_Dipeptide_transport_ATP-binding_protein_dppF_2014501..2014731_POSITIVE 187 89 43 45 9 NC_003454:FN0645|5end_Porphobilinogen_deaminase_1302264..1302494_NEGATIVE 187 123 81 104 61 NC_003454:FN1742|5end_V-type_sodium_ATP_synthase_subunit_G_240790..241020_NEGATIVE 186 125 86 62 10 NC_003454:FN0751|5end_L-asparaginase_I_1410731..1410961_NEGATIVE 186 128 81 47 12 NC_003454:FN0719|5end_Hypothetical_cytosolic_protein_1375924..1376154_POSITIVE 186 120 77 144 98 NC_003454:FN0717|5end_Ribosomal_small_subunit_pseudouridine_synthase_A_1374913..1375143_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 240 63 21 94 50 NC_003454:FN0610|3end_hypothetical_protein_1268362..1268512_POSITIVE 213 126 81 52 13 NC_003454:FN1585|3end_hypothetical_protein_96213..96363_NEGATIVE 206 128 85 90 43 NC_003454:FN1355|3end_Integral_membrane_protein_2006679..2006829_NEGATIVE 206 137 97 53 14 NC_003454:FN0205|3end_Sodium/glutamate_symport_carrier_protein_832808..832958_POSITIVE 205 125 84 60 13 NC_003454:FN0175|3end_Cell_division_inhibitor_MinC_801235..801385_POSITIVE 204 127 109 43 19 NC_003454:FN0227|3end_hypothetical_protein_854114..854264_NEGATIVE 198 69 26 52 12 NC_003454:FN1750|3end_Pyruvate-flavodoxin_oxidoreductase_248079..248229_POSITIVE 186 125 86 72 20 NC_003454:FN0752|3end_Proline_iminopeptidase_1410721..1410871_NEGATIVE 186 128 81 47 12 NC_003454:FN0718|3end_hypothetical_protein_1376004..1376154_POSITIVE 186 120 77 144 98 NC_003454:FN0716|3end_Phophatidylinositol-4-phosphate_5-kinase_1374993..1375143_POSITIVE 184 128 84 79 37 NC_003454:FN1000|3end_biotin_synthase_1656101..1656251_POSITIVE 182 68 36 146 115 NC_003454:FN0580|3end_Penicillin-binding_protein_1237184..1237334_POSITIVE 182 63 25 132 99 NC_003454:FN0335|3end_Outer_membrane_porin_F_969157..969307_NEGATIVE 181 127 81 134 90 NC_003454:FN1466|3end_hypothetical_protein_2149226..2149376_POSITIVE 180 123 97 89 63 NC_003454:FN1519|3end_23S_rRNA_methyltransferase_24088..24238_NEGATIVE 179 37 8 151 114 NC_003454:FN0816|3end_dehydrogenase_with_MaoC-like_domain_1476455..1476605_POSITIVE 178 119 78 147 108 NC_003454:FN0964|3end_Precorrin-8W_decarboxylase_1617737..1617887_NEGATIVE 177 70 23 127 81 NC_003454:FN1189|3end_hypothetical_protein_1851750..1851900_POSITIVE 176 132 114 78 58 NC_003454:FN1297|3end_Methionine_aminopeptidase_1954217..1954367_NEGATIVE 176 126 81 108 63 NC_003454:FN1846|3end_hypothetical_protein_336225..336375_POSITIVE