Origin IGS: tctgttttgagtgagatgttagtatggccgacggccggcattgcacaccaacaactctctctgtgcataaccttccgagggacctttccgtcctaataattccgaaaaaggaaagaaatggattgaataatgtgtgtccgatagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actatcggacacacattattcaatccatttctttcctttttcggaattattaggacggaaaggtccctcggaaggttatgcacagagagagttgttggtgtgcaatgccggccgtcggccatactaacatctcactcaaaacaga Mask Tandem Repeat Region ================================================ tctgttttgagtgagatgttagtatggccgacggccggcattgcacaccaacaactctctctgtgcataaccttccgagggacctttccgtcctaataattccgaaaaaggaaagaaatggattgaataatgtgtgtccgatagt Find is-nt database================================================ Query_seq: PG0086:PG0087|PG0086:PG0087:ATP-dependent RNA helicase, DEAD/DEAH box family:SIS domain protein:<-<-:102450..102594 145 tctgttttgagtgagatgttagtatggccgacggccggcattgcacaccaacaactctctctgtgcataaccttccgagggacctttccgtcctaataattccgaaaaaggaaagaaatggattgaataatgtgtgtccgatagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0086:PG0087|PG0086:PG0087:ATP-dependent RNA helicase, DEAD/DEAH box family:SIS domain protein:<-<-:102450..102594 145 tctgttttgagtgagatgttagtatggccgacggccggcattgcacaccaacaactctctctgtgcataaccttccgagggacctttccgtcctaataattccgaaaaaggaaagaaatggattgaataatgtgtgtccgatagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0086:PG0087|PG0086:PG0087:ATP-dependent RNA helicase, DEAD/DEAH box family:SIS domain protein:<-<-:102450..102594 145 tctgttttgagtgagatgttagtatggccgacggccggcattgcacaccaacaactctctctgtgcataaccttccgagggacctttccgtcctaataattccgaaaaaggaaagaaatggattgaataatgtgtgtccgatagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctgttttgagtgagatgttagtatggccgacggccggcattgcacaccaacaactctctctgtgcataaccttccgagggacctttccgtcctaataattccgaaaaaggaaagaaatggattgaataatgtgtgtccgatagt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 24 End: 143 ....................... M A D G R H C T P T T L S V H N L P R D L S V L I I P K K E R N G L N N V C P I .. Protein_Len: 34 Strand: - Start: 22 End: 123 ..................... Y P R R G A N C V L L E R Q A Y G E S P G K R G L L E S F P F F H M ...................... Protein_Len: 47 Strand: - Start: 2 End: 142 . Q K S H S T L I A S P R C Q V G V V R E T C L R G L S R E T R I I G F F S L F P N F L T H G M ... tctgttttgagtgagatgttagtatggccgacggccggcattgcacaccaacaactctctctgtgcataaccttccgagggacctttccgtcctaataattccgaaaaaggaaagaaatggattgaataatgtgtgtccgatagt 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================================================ tctgttttgagtgagatgttagtatggccgacggccggcattgcacaccaacaactctctctgtgcataaccttccgagggacctttccgtcctaataattccgaaaaaggaaagaaatggattgaataatgtgtgtccgatagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0086:PG0087|PG0086:PG0087:ATP-dependent RNA helicase, DEAD/DEAH box family:SIS domain protein:<-<-:102450..102594 145 tctgttttgagtgagatgttagtatggccgacggccggcattgcacaccaacaactctctctgtgcataaccttccgagggacctttccgtcctaataattccgaaaaaggaaagaaatggattgaataatgtgtgtccgatagt Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_002950_PG0086_PG0087|ATP-dependent RNA helicase, DEAD/DEAH box family:SIS domain protein|NEGATIVE:NEGATIVE|[102450,102594]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 tctgttttgagtgagatgttagtatggccgacggccggcattgcacaccaacaactctctctgtgcataaccttccgagggacctttccgtcctaataattccgaaaaaggaaagaaatggattgaataatgtgtgtccgatagt tctgttttgagtgagatgttagtatggccgacggccggcattgcacaccaacaactctctctgtgcataaccttccgagggacctttccgtcctaataattccgaaaaaggaaagaaatggattgaataatgtgtgtccgatagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUGUUUUGAGUGAGAUGUUAGUAUGGCCGACGGCCGGCAUUGCACACCAACAACUCUCUCUGUGCAUAACCUUCCGAGGGACCUUUCCGUCCUAAUAAUUCCGAAAAAGGAAAGAAAUGGAUUGAAUAAUGUGUGUCCGAUAGU ..(((...(((.(((.((((.((.((((((.....))))....)).)).)))).))).)))...)))..((..((.((.(.((..(((.((((......((((......))))......)))).)))....)).).)).))..)) (-35.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAUCGGACACACAUUAUUCAAUCCAUUUCUUUCCUUUUUCGGAAUUAUUAGGACGGAAAGGUCCCUCGGAAGGUUAUGCACAGAGAGAGUUGUUGGUGUGCAAUGCCGGCCGUCGGCCAUACUAACAUCUCACUCAAAACAGA ......((((........(((..(((......((((......))))......)))..)))..)))).((....)).........(((.(((.((((((((((....((((.....)))))))))))))).))).)))........ (-38.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1058 80 31 171 122 NC_002950:PG0086|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_102359..102589_NEGATIVE 377 44 6 213 178 NC_002950:PG1579|5end_ATPase,_MoxR_family_1656493..1656723_POSITIVE 374 41 1 73 27 NC_002950:PG2105|5end_lipoprotein,_putative_2213999..2214229_POSITIVE 362 80 34 54 4 NC_002950:PG0094|5end_outer_membrane_efflux_protein,_putative_111193..111423_NEGATIVE 357 66 25 111 71 NC_002950:PG1311|5end_hypothetical_protein_1389709..1389939_POSITIVE 353 48 10 204 158 NC_002950:PG1784|5end_hypothetical_protein_1872566..1872796_POSITIVE 350 50 2 176 122 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 347 48 8 165 129 NC_002950:PG0043|5end_beta-hexosaminidase_51066..51296_POSITIVE 343 77 33 185 124 NC_002950:PG1521|5end_O-succinylbenzoic_acid--CoA_ligase_1599103..1599333_NEGATIVE 342 67 22 195 142 NC_002950:PG0744|5end_RNA_methyltransferase,_TrmH_family_791897..792127_NEGATIVE 342 66 25 212 150 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 341 50 25 37 15 NC_002950:PG2092|5end_hypothetical_protein_2192910..2193140_NEGATIVE 336 93 52 172 124 NC_002950:PG1370|5end_lysyl-tRNA_synthetase_1452229..1452459_NEGATIVE 332 46 1 202 144 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 332 80 33 191 148 NC_002950:PG2048|5end_hypothetical_protein_2148514..2148744_NEGATIVE 331 56 11 215 172 NC_002950:PG0271|5end_single-stranded_binding_protein_303842..304072_POSITIVE 331 79 32 96 39 NC_002950:PG0123|5end_hypothetical_protein_144987..145217_POSITIVE 330 44 8 40 6 NC_002950:PG2006|5end_hypothetical_protein_2094587..2094817_POSITIVE 329 49 1 159 108 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 329 96 51 66 10 NC_002950:PG1931|5end_50S_ribosomal_protein_L16_2020849..2021079_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 49 2 50 1 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 377 44 6 112 77 NC_002950:PG1578|3end_quinolinate_synthetase_1656472..1656622_POSITIVE 357 66 25 148 108 NC_002950:PG1310|3end_exsB_protein_1389826..1389976_POSITIVE 343 89 47 58 5 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 342 67 22 110 57 NC_002950:PG0745|3end_lactoylglutathione_lyase,_putative_791982..792132_NEGATIVE 340 48 1 123 67 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 337 44 2 56 7 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 336 93 52 49 1 NC_002950:PG1371|3end_phosphorylase_family_protein_1452352..1452502_NEGATIVE 327 59 26 142 94 NC_002950:PG0003|3end_hypothetical_protein_1919..2069_NEGATIVE 326 77 32 129 99 NC_002950:PG2205|3end_2-dehydropantoate_2-reductase_2317145..2317295_POSITIVE 324 51 13 61 15 NC_002950:PG2001|3end_signal_peptidase_I_2089458..2089608_NEGATIVE 318 90 42 81 27 NC_002950:PG1115|3end_signal_recognition_particle_protein_1188887..1189037_POSITIVE 318 49 18 38 7 NC_002950:PG0735|3end_aminotransferase,_class_V_785677..785827_POSITIVE 317 38 1 132 86 NC_002950:PG0897|3end_alpha-amylase_family_protein_960868..961018_NEGATIVE 313 94 55 48 2 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 311 45 18 39 12 NC_002950:PG1848|3end_RNA_methyltransferase,_TrmH_family_1946633..1946783_NEGATIVE 311 49 1 136 64 NC_002950:PG1589|3end_dihydropteroate_synthase_1666593..1666743_NEGATIVE 309 68 22 86 40 NC_002950:PG0632|3end_biopolymer_transport_protein_ExbD,_putative_685376..685526_POSITIVE 307 66 21 75 19 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 307 47 17 34 3 NC_002950:PG0327|3end_hypothetical_protein_360907..361057_NEGATIVE