Origin IGS: ttttcttttcataatttaatacatccttaactttactttgttctttaagagtaaaaatactccatagaaaaattatcaataataaaaacgacaagattttgtcgttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaacgacaaaatcttgtcgtttttattattgataatttttctatggagtatttttactcttaaagaacaaagtaaagttaaggatgtattaaattatgaaaagaaaa Mask Tandem Repeat Region ================================================ ttttcttttcataatttaatacatccttaactttactttgttctttaagagtaaaaatactccatagaaaaattatcaataataaaaacgacaagattttgtcgttt Find is-nt database================================================ Query_seq: FN1334:FN1335|FN1334:FN1335:N-acetylmuramoyl-L-alanine amidase:Protein translocase subunit YajC:<-<-:1988710..1988816 107 ttttcttttcataatttaatacatccttaactttactttgttctttaagagtaaaaatactccatagaaaaattatcaataataaaaacgacaagattttgtcgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1334:FN1335|FN1334:FN1335:N-acetylmuramoyl-L-alanine amidase:Protein translocase subunit YajC:<-<-:1988710..1988816 107 ttttcttttcataatttaatacatccttaactttactttgttctttaagagtaaaaatactccatagaaaaattatcaataataaaaacgacaagattttgtcgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1334:FN1335|FN1334:FN1335:N-acetylmuramoyl-L-alanine amidase:Protein translocase subunit YajC:<-<-:1988710..1988816 107 ttttcttttcataatttaatacatccttaactttactttgttctttaagagtaaaaatactccatagaaaaattatcaataataaaaacgacaagattttgtcgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcttttcataatttaatacatccttaactttactttgttctttaagagtaaaaatactccatagaaaaattatcaataataaaaacgacaagattttgtcgttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 2 End: 97 . K K E Y N L V D K V K S Q E K L T F I S W L F I I L L L F S L M .......... ttttcttttcataatttaatacatccttaactttactttgttctttaagagtaaaaatactccatagaaaaattatcaataataaaaacgacaagattttgtcgttt 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================================================ ttttcttttcataatttaatacatccttaactttactttgttctttaagagtaaaaatactccatagaaaaattatcaataataaaaacgacaagattttgtcgttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1334:FN1335|FN1334:FN1335:N-acetylmuramoyl-L-alanine amidase:Protein translocase subunit YajC:<-<-:1988710..1988816 107 ttttcttttcataatttaatacatccttaactttactttgttctttaagagtaaaaatactccatagaaaaattatcaataataaaaacgacaagattttgtcgttt Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_003454_FN1334_FN1335|N-acetylmuramoyl-L-alanine amidase:Protein translocase subunit YajC|NEGATIVE:NEGATIVE|[1988710,1988816]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttttcttttcataatttaatacatccttaactttactttgttctttaagagtaaaaatactccatagaaaaattatcaataataaaaacgacaagattttgtcgttt ttttcttttcataatttaatacatccttaactttactttgttctttaagagtaaaaatactccatagaaaaattatcaataataaaaacgacaagattttgtcgttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUUUCAUAAUUUAAUACAUCCUUAACUUUACUUUGUUCUUUAAGAGUAAAAAUACUCCAUAGAAAAAUUAUCAAUAAUAAAAACGACAAGAUUUUGUCGUUU ..........(((((((..............((((((((........))))))))..............))))))).........(((((((((....))))))))) (-14.19) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACGACAAAAUCUUGUCGUUUUUAUUAUUGAUAAUUUUUCUAUGGAGUAUUUUUACUCUUAAAGAACAAAGUAAAGUUAAGGAUGUAUUAAAUUAUGAAAAGAAAA (((((((((....))))))))).((((.(((((.((((((((..((((((....))))))...)))..)))))...))))).))))..................... (-18.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 712 70 21 161 112 NC_003454:FN1334|5end_N-acetylmuramoyl-L-alanine_amidase_1988619..1988849_NEGATIVE 207 47 13 231 197 NC_003454:FN2010|5end_Transcriptional_regulator,_MarR_family_510302..510532_NEGATIVE 203 67 22 93 46 NC_003454:FN1915|5end_Anti-sigma_B_factor_412320..412550_NEGATIVE 193 66 22 207 153 NC_003454:FN2092|5end_Integral_membrane_protein_603111..603341_NEGATIVE 187 42 6 131 94 NC_003454:FN1655|5end_Hypothetical_cytosolic_protein_150898..151128_POSITIVE 181 50 4 136 96 NC_003454:FN1412|5end_5-methylthioribose_kinase_2073206..2073436_NEGATIVE 177 71 37 178 149 NC_003454:FN0566|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1218482..1218712_NEGATIVE 176 51 24 34 2 NC_003454:FN1920|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_416910..417140_NEGATIVE 172 47 1 182 138 NC_003454:FN1318|5end_RNA_polymerase_sigma_factor_rpoD_1972096..1972326_NEGATIVE 172 38 1 110 80 NC_003454:FN0505|5end_Anthranilate_synthase_component_II_1155775..1156005_NEGATIVE 170 37 1 178 142 NC_003454:FN1914|5end_Anti-sigma_F_factor_antagonist_411990..412220_NEGATIVE 169 50 1 159 118 NC_003454:FN1414|5end_NA+/H+_antiporter_NHAC_2075559..2075789_NEGATIVE 169 42 1 49 7 NC_003454:FN1224|5end_2-dehydro-3-deoxyphosphooctonate_aldolase_1883400..1883630_NEGATIVE 169 68 24 114 57 NC_003454:FN0926|5end_GTP_pyrophosphokinase_1580812..1581042_POSITIVE 167 50 4 129 83 NC_003454:FN0750|5end_hypothetical_protein_1409705..1409935_NEGATIVE 165 49 1 144 95 NC_003454:FN1345|5end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase_1998957..1999187_NEGATIVE 163 36 10 189 165 NC_003454:FN1379|5end_Citrate_lyase_beta_chain_2026355..2026585_POSITIVE 161 67 24 93 42 NC_003454:FN0922|5end_Homoserine_kinase_1577526..1577756_NEGATIVE 161 69 35 79 48 NC_003454:FN0370|5end_Signal_peptidase_I_999832..1000062_NEGATIVE 161 53 22 41 2 NC_003454:FN1681|5end_hypothetical_protein_176562..176792_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 235 50 13 103 66 NC_003454:FN2011|3end_Valyl-tRNA_synthetase_510433..510583_NEGATIVE 199 47 5 130 84 NC_003454:FN0065|3end_Transcription_accessory_protein_(S1_RNA_binding_domain)_702184..702334_POSITIVE 195 50 1 96 55 NC_003454:FN0023|3end_Short-chain_fatty_acids_transporter_662780..662930_POSITIVE 186 53 22 118 87 NC_003454:FN2044|3end_LSU_ribosomal_protein_L33P_549957..550107_NEGATIVE 181 50 4 121 81 NC_003454:FN1413|3end_translation_initiation_factor_IF-2B_subunit_alpha_2073221..2073371_NEGATIVE 176 51 24 34 2 NC_003454:FN1921|3end_Biotin_operon_repressor_416910..417060_NEGATIVE 172 38 1 83 53 NC_003454:FN0506|3end_Arginyl-tRNA_synthetase_1155802..1155952_NEGATIVE 169 50 1 110 69 NC_003454:FN1415|3end_NADH-dependent_butanol_dehydrogenase_A_2075608..2075758_NEGATIVE 169 42 1 83 41 NC_003454:FN1225|3end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--meso-_lanthionine_ligase_1883366..1883516_NEGATIVE 169 68 24 101 44 NC_003454:FN0925|3end_hypothetical_protein_1580879..1581029_POSITIVE 167 50 4 113 67 NC_003454:FN0751|3end_L-asparaginase_I_1409721..1409871_NEGATIVE 165 49 1 124 75 NC_003454:FN1346|3end_Hypothetical_cytosolic_protein_1998977..1999127_NEGATIVE 164 76 40 80 37 NC_003454:FN0141|3end_hypothetical_protein_773203..773353_NEGATIVE 161 67 24 81 30 NC_003454:FN0923|3end_Cardiolipin_synthetase_1577538..1577688_NEGATIVE 161 53 22 115 76 NC_003454:FN1681|3end_hypothetical_protein_176488..176638_NEGATIVE 158 42 1 121 81 NC_003454:FN0159|3end_hypothetical_protein_788329..788479_POSITIVE 156 51 15 97 53 NC_003454:FN1507|3end_riboflavin_synthase_subunit_alpha_12908..13058_POSITIVE 154 44 1 121 75 NC_003454:FN1053|3end_hypothetical_protein_1701651..1701801_POSITIVE 154 68 29 43 6 NC_003454:FN0722|3end_WD-repeat_family_protein_1381604..1381754_POSITIVE 154 63 31 78 48 NC_003454:FN0448|3end_DNA-repair_protein_1092747..1092897_POSITIVE