Origin IGS: aaattttaaagaaaactttttcattaaaatctcctcctaggtatatttttaaattttggtatattttctattatatcaaaaaatattttaaaatcaatataaaaataaaaacaacatccacagacatagatgttattttgttcttctttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaagaagaacaaaataacatctatgtctgtggatgttgtttttatttttatattgattttaaaatattttttgatataatagaaaatataccaaaatttaaaaatatacctaggaggagattttaatgaaaaagttttctttaaaattt Mask Tandem Repeat Region ================================================ aaattttaaagaaaactttttcattaaaatctcctcctaggtatatttttaaattttggtatattttctattatatcaaaaaatattttaaaatcaatataaaaataaaaacaacatccacagacatagatgttattttgttcttctttt Find is-nt database================================================ Query_seq: FN0034:FN0035|FN0034:FN0035:hypothetical protein:hypothetical protein:<-<-:676180..676329 150 aaattttaaagaaaactttttcattaaaatctcctcctaggtatatttttaaattttggtatattttctattatatcaaaaaatattttaaaatcaatataaaaataaaaacaacatccacagacatagatgttattttgttcttctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0034:FN0035|FN0034:FN0035:hypothetical protein:hypothetical protein:<-<-:676180..676329 150 aaattttaaagaaaactttttcattaaaatctcctcctaggtatatttttaaattttggtatattttctattatatcaaaaaatattttaaaatcaatataaaaataaaaacaacatccacagacatagatgttattttgttcttctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0034:FN0035|FN0034:FN0035:hypothetical protein:hypothetical protein:<-<-:676180..676329 150 aaattttaaagaaaactttttcattaaaatctcctcctaggtatatttttaaattttggtatattttctattatatcaaaaaatattttaaaatcaatataaaaataaaaacaacatccacagacatagatgttattttgttcttctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattttaaagaaaactttttcattaaaatctcctcctaggtatatttttaaattttggtatattttctattatatcaaaaaatattttaaaatcaatataaaaataaaaacaacatccacagacatagatgttattttgttcttctttt Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 3 End: 149 .. M L K K T F S L K S P P R Y I F K F W Y I F Y Y I K K Y F K I N I K I K T T S T D I D V I L F F F . Protein_Len: 35 Strand: - Start: 27 End: 131 .......................... F R R R P I N K F K P I N E I I D F F I K F D I Y F Y F C C G C V Y M ................... aaattttaaagaaaactttttcattaaaatctcctcctaggtatatttttaaattttggtatattttctattatatcaaaaaatattttaaaatcaatataaaaataaaaacaacatccacagacatagatgttattttgttcttctttt 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================================================ aaattttaaagaaaactttttcattaaaatctcctcctaggtatatttttaaattttggtatattttctattatatcaaaaaatattttaaaatcaatataaaaataaaaacaacatccacagacatagatgttattttgttcttctttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0034:FN0035|FN0034:FN0035:hypothetical protein:hypothetical protein:<-<-:676180..676329 150 aaattttaaagaaaactttttcattaaaatctcctcctaggtatatttttaaattttggtatattttctattatatcaaaaaatattttaaaatcaatataaaaataaaaacaacatccacagacatagatgttattttgttcttctttt Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: NC_003454_FN0034_FN0035|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[676180,676329]|150 HSP 1 e-value: 6.0E-15 bit: 81.8 Len: 41 Query Start:1 Query End:41 Subject Strand: POSITIVE Subject Start: 1 Subject End: 41 aaattttaaagaaaactttttcattaaaatctcctcctagg............................................................................................................. aaattttaaagaaaactttttcattaaaatctcctcctagg............................................................................................................. HSP 2 e-value: 9.0E-14 bit: 77.8 Len: 39 Query Start:112 Query End:150 Subject Strand: POSITIVE Subject Start: 112 Subject End: 150 ...............................................................................................................caacatccacagacatagatgttattttgttcttctttt ...............................................................................................................caacatccacagacatagatgttattttgttcttctttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUUAAAGAAAACUUUUUCAUUAAAAUCUCCUCCUAGGUAUAUUUUUAAAUUUUGGUAUAUUUUCUAUUAUAUCAAAAAAUAUUUUAAAAUCAAUAUAAAAAUAAAAACAACAUCCACAGACAUAGAUGUUAUUUUGUUCUUCUUUU ..(((((((((............((((((...((.....)).....)))))).((((((((((........))))))))))....))))))))).........(((((((..((((((..........)))))).)))))))........ (-18.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGAAGAACAAAAUAACAUCUAUGUCUGUGGAUGUUGUUUUUAUUUUUAUAUUGAUUUUAAAAUAUUUUUUGAUAUAAUAGAAAAUAUACCAAAAUUUAAAAAUAUACCUAGGAGGAGAUUUUAAUGAAAAAGUUUUCUUUAAAAUUU ...........((((((((((((((....))))))))))))))((((((((....((((((...((((((((((......))))))))))...))))))))))))))......((((((((((((......))))))))))))....... (-29.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 677 60 11 151 102 NC_003454:FN0034|5end_hypothetical_protein_676089..676319_NEGATIVE 282 58 14 137 81 NC_003454:FN0897|5end_Hypothetical_cytosolic_protein_1555833..1556063_POSITIVE 276 60 15 131 81 NC_003454:FN0796|5end_pyruvate_phosphate_dikinase_1453008..1453238_POSITIVE 263 47 4 116 64 NC_003454:FN0472|5end_flavodoxin_1118165..1118395_NEGATIVE 262 80 33 147 97 NC_003454:FN1677|5end_Transposase_174224..174454_NEGATIVE 253 38 4 105 77 NC_003454:FN2071|5end_hypothetical_protein_582375..582605_NEGATIVE 241 58 16 166 119 NC_003454:FN0049|5end_hypothetical_protein_686351..686581_POSITIVE 235 49 14 154 120 NC_003454:FN2121|5end_Hypothetical_exported_24-amino_acid_repeat_protein_629728..629958_NEGATIVE 233 40 1 108 74 NC_003454:FN1252|5end_34_kDa_membrane_antigen_precursor_1909368..1909598_POSITIVE 233 50 4 122 73 NC_003454:FN0366|5end_Phosphoacetylglucosamine_mutase_996366..996596_NEGATIVE 229 67 21 129 88 NC_003454:FN0154|5end_Ribonuclease_G_781740..781970_POSITIVE 225 38 12 104 81 NC_003454:FN0487|5end_D-lactate_dehydrogenase_1132772..1133002_NEGATIVE 222 57 17 166 120 NC_003454:FN0872|5end_hypothetical_protein_1532647..1532877_NEGATIVE 219 80 32 140 96 NC_003454:FN1620|5end_30S_ribosomal_protein_S2_127896..128126_POSITIVE 216 70 21 137 88 NC_003454:FN1725|5end_Potassium_uptake_protein_KtrB_224671..224901_NEGATIVE 213 129 86 194 147 NC_003454:FN0283|5end_tRNA_(Guanine-N1)_-methyltransferase_913405..913635_NEGATIVE 212 48 14 114 81 NC_003454:FN1165|5end_D-galactose-binding_protein_1822898..1823128_POSITIVE 211 65 21 134 88 NC_003454:FN0692|5end_Nitrogen_regulation_protein_NIFR3_1346428..1346658_POSITIVE 211 68 22 127 89 NC_003454:FN0673|5end_EBSC_protein_1328984..1329214_POSITIVE 210 57 18 174 134 NC_003454:FN1363|5end_Dipeptide_transport_ATP-binding_protein_dppF_2014501..2014731_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 404 150 102 90 42 NC_003454:FN0034|3end_hypothetical_protein_675439..675589_NEGATIVE 336 38 1 54 17 NC_003454:FN0036|3end_Hypothetical_membrane-spanning_Protein_676977..677127_NEGATIVE 276 60 15 119 69 NC_003454:FN0795|3end_CBS_domain_containing_protein_1453076..1453226_POSITIVE 235 49 14 84 50 NC_003454:FN2122|3end_Phenylalanyl-tRNA_synthetase_beta_chain_629798..629948_NEGATIVE 233 40 1 49 15 NC_003454:FN1251|3end_High-affinity_iron_permease_1909389..1909539_POSITIVE 233 50 4 105 56 NC_003454:FN0367|3end_Integral_membrane_protein_996383..996533_NEGATIVE 223 69 21 112 68 NC_003454:FN0807|3end_3-deoxy-manno-octulosonate_cytidylyltransferase_1467157..1467307_NEGATIVE 222 57 17 110 64 NC_003454:FN0873|3end_Protease_IV_1532703..1532853_NEGATIVE 216 70 21 122 73 NC_003454:FN1726|3end_Na+_driven_multidrug_efflux_pump_224686..224836_NEGATIVE 211 68 22 105 67 NC_003454:FN0672|3end_ATPase_1329042..1329192_POSITIVE 207 70 31 62 19 NC_003454:FN0411|3end_hypothetical_protein_1048616..1048766_POSITIVE 202 64 21 151 113 NC_003454:FN0153|3end_Oxygen-independent_coproporphyrinogen_III_oxidase_781845..781995_POSITIVE 201 56 16 141 96 NC_003454:FN0237|3end_ABC_transporter_permease_protein_861403..861553_NEGATIVE 198 42 17 44 23 NC_003454:FN1256|3end_C4-dicarboxylate_transporter_large_subunit_1911920..1912070_NEGATIVE 198 52 18 104 75 NC_003454:FN0416|3end_Type_III_restriction-modification_system_methylation_subunit_1055957..1056107_POSITIVE 198 41 4 114 68 NC_003454:FN1688|3end_Oxidoreductase_183697..183847_NEGATIVE 196 78 34 130 95 NC_003454:FN1312|3end_Biopolymer_transport_exbB_protein_1966340..1966490_NEGATIVE 196 45 9 97 62 NC_003454:FN1178|3end_Hypothetical_cytosolic_protein_1838793..1838943_NEGATIVE 195 53 16 112 72 NC_003454:FN1739|3end_V-type_sodium_ATP_synthase_subunit_E_237351..237501_NEGATIVE 194 60 19 151 109 NC_003454:FN1727|3end_Chloride_channel_protein_226062..226212_NEGATIVE