Origin IGS: tcaaacgcacaacatatcggctttctgcttgaaaaaggcgattggattcatctccgaagcatgattatcgtatctgatcgatctaatgttcgtggcagggtagggatccggcattttctcttctccatttctaacttttatgagaccatagtatcctctcatgttagaccatagtatcctctcatatgagaccatagtatcctatccatatcggtcatactttcttcacgatatggatttcactaatgaatatccgaatactatggatacaactatctcagagatgggaggtggccttcgctgaaatgcgatacgaggagtgtgggtaatgccgttagg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 cctaacggcattacccacactcctcgtatcgcatttcagcgaaggccacctcccatctctgagatagttgtatccatagtattcggatattcattagtgaaatccatatcgtgaagaaagtatgaccgatatggataggatactatggtctcatatgagaggatactatggtctaacatgagaggatactatggtctcataaaagttagaaatggagaagagaaaatgccggatccctaccctgccacgaacattagatcgatcagatacgataatcatgcttcggagatgaatccaatcgcctttttcaagcagaaagccgatatgttgtgcgtttga Mask Tandem Repeat Region ================================================ tcaaacgcacaacatatcggctttctgcttgaaaaaggcgattggattcatctccgaagcatgattatcgtatctgatcgatctaatgttcgtggcagggtagggatccggcattttctcttctccatttctaactttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatccatatcggtcatactttcttcacgatatggatttcactaatgaatatccgaatactatggatacaactatctcagagatgggaggtggccttcgctgaaatgcgatacgaggagtgtgggtaatgccgttagg Find is-nt database================================================ Query_seq: PG0807:PG0809|PG0807:PG0809:NusB family protein:hypothetical protein:<-<-:864815..865153 339 tcaaacgcacaacatatcggctttctgcttgaaaaaggcgattggattcatctccgaagcatgattatcgtatctgatcgatctaatgttcgtggcagggtagggatccggcattttctcttctccatttctaacttttatgagaccatagtatcctctcatgttagaccatagtatcctctcatatgagaccatagtatcctatccatatcggtcatactttcttcacgatatggatttcactaatgaatatccgaatactatggatacaactatctcagagatgggaggtggccttcgctgaaatgcgatacgaggagtgtgggtaatgccgttagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0807:PG0809|PG0807:PG0809:NusB family protein:hypothetical protein:<-<-:864815..865153 339 tcaaacgcacaacatatcggctttctgcttgaaaaaggcgattggattcatctccgaagcatgattatcgtatctgatcgatctaatgttcgtggcagggtagggatccggcattttctcttctccatttctaacttttatgagaccatagtatcctctcatgttagaccatagtatcctctcatatgagaccatagtatcctatccatatcggtcatactttcttcacgatatggatttcactaatgaatatccgaatactatggatacaactatctcagagatgggaggtggccttcgctgaaatgcgatacgaggagtgtgggtaatgccgttagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0807:PG0809|PG0807:PG0809:NusB family protein:hypothetical protein:<-<-:864815..865153 339 tcaaacgcacaacatatcggctttctgcttgaaaaaggcgattggattcatctccgaagcatgattatcgtatctgatcgatctaatgttcgtggcagggtagggatccggcattttctcttctccatttctaacttttatgagaccatagtatcctctcatgttagaccatagtatcctctcatatgagaccatagtatcctatccatatcggtcatactttcttcacgatatggatttcactaatgaatatccgaatactatggatacaactatctcagagatgggaggtggccttcgctgaaatgcgatacgaggagtgtgggtaatgccgttagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaaacgcacaacatatcggctttctgcttgaaaaaggcgattggattcatctccgaagcatgattatcgtatctgatcgatctaatgttcgtggcagggtagggatccggcattttctcttctccatttctaacttttatgagaccatagtatcctctcatgttagaccatagtatcctctcatatgagaccatagtatcctatccatatcggtcatactttcttcacgatatggatttcactaatgaatatccgaatactatggatacaactatctcagagatgggaggtggccttcgctgaaatgcgatacgaggagtgtgggtaatgccgttagg Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 16 End: 171 ............... M G F L L E K G D W I H L R S M I I V S D R S N V R G R V G I R H F L F S I S N F Y E T I V S S H V R P ........................................................................................................................................................................ Protein_Len: 47 Strand: + Start: 161 End: 301 ................................................................................................................................................................ M L D H S I L S Y E T I V S Y P Y R S Y F L H D M D F T N E Y P N T M D T T I S E M G G G L R ...................................... Protein_Len: 41 Strand: + Start: 204 End: 326 ........................................................................................................................................................................................................... M H I G H T F F T I W I S L M N I R I L W I Q L S Q R W E V A F A E M R Y E E C G ............. Protein_Len: 30 Strand: + Start: 250 End: 339 ......................................................................................................................................................................................................................................................... M S E Y Y G Y N Y L R D G R W P S L K C D T R S V G N A V R Protein_Len: 34 Strand: - Start: 229 End: 330 .................................................................................................................................................................................................................................... S I S K V L S Y G F V I S V V I E S I P P P R R Q F A I R P T H T M ......... Protein_Len: 60 Strand: - Start: 4 End: 195 ... D A K Q K F F A I P N M E S A H N D Y R I S R I N T A P Y P D P M K E E G N R V K I L G Y Y G R M N S W L I R E Y S V M ................................................................................................................................................ tcaaacgcacaacatatcggctttctgcttgaaaaaggcgattggattcatctccgaagcatgattatcgtatctgatcgatctaatgttcgtggcagggtagggatccggcattttctcttctccatttctaacttttatgagaccatagtatcctctcatgttagaccatagtatcctctcatatgagaccatagtatcctatccatatcggtcatactttcttcacgatatggatttcactaatgaatatccgaatactatggatacaactatctcagagatgggaggtggccttcgctgaaatgcgatacgaggagtgtgggtaatgccgttagg 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================================================ tcaaacgcacaacatatcggctttctgcttgaaaaaggcgattggattcatctccgaagcatgattatcgtatctgatcgatctaatgttcgtggcagggtagggatccggcattttctcttctccatttctaacttttatgagaccatagtatcctctcatgttagaccatagtatcctctcatatgagaccatagtatcctatccatatcggtcatactttcttcacgatatggatttcactaatgaatatccgaatactatggatacaactatctcagagatgggaggtggccttcgctgaaatgcgatacgaggagtgtgggtaatgccgttagg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0807:PG0809|PG0807:PG0809:NusB family protein:hypothetical protein:<-<-:864815..865153 339 tcaaacgcacaacatatcggctttctgcttgaaaaaggcgattggattcatctccgaagcatgattatcgtatctgatcgatctaatgttcgtggcagggtagggatccggcattttctcttctccatttctaacttttatgagaccatagtatcctctcatgttagaccatagtatcctctcatatgagaccatagtatcctatccatatcggtcatactttcttcacgatatggatttcactaatgaatatccgaatactatggatacaactatctcagagatgggaggtggccttcgctgaaatgcgatacgaggagtgtgggtaatgccgttagg Intra-Species Hit: Count: 1 Min: 1 Max: 339 Len: 339 Subject: NC_002950_PG0807_PG0809|NusB family protein:hypothetical protein|NEGATIVE:NEGATIVE|[864815,865153]|339 HSP 1 e-value: 0.0 bit: 672.0 Len: 339 Query Start:1 Query End:339 Subject Strand: POSITIVE Subject Start: 1 Subject End: 339 tcaaacgcacaacatatcggctttctgcttgaaaaaggcgattggattcatctccgaagcatgattatcgtatctgatcgatctaatgttcgtggcagggtagggatccggcattttctcttctccatttctaacttttatgagaccatagtatcctctcatgttagaccatagtatcctctcatatgagaccatagtatcctatccatatcggtcatactttcttcacgatatggatttcactaatgaatatccgaatactatggatacaactatctcagagatgggaggtggccttcgctgaaatgcgatacgaggagtgtgggtaatgccgttagg tcaaacgcacaacatatcggctttctgcttgaaaaaggcgattggattcatctccgaagcatgattatcgtatctgatcgatctaatgttcgtggcagggtagggatccggcattttctcttctccatttctaacttttatgagaccatagtatcctctcatgttagaccatagtatcctctcatatgagaccatagtatcctatccatatcggtcatactttcttcacgatatggatttcactaatgaatatccgaatactatggatacaactatctcagagatgggaggtggccttcgctgaaatgcgatacgaggagtgtgggtaatgccgttagg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAACGCACAACAUAUCGGCUUUCUGCUUGAAAAAGGCGAUUGGAUUCAUCUCCGAAGCAUGAUUAUCGUAUCUGAUCGAUCUAAUGUUCGUGGCAGGGUAGGGAUCCGGCAUUUUCUCUUCUCCAUUUCUAACUUUUAUGAGACCAUAGUAUCCUCUCAUGUUAGACCAUAGUAUCCUCUCAUAUGAGACCAUAGUAUCCUAUCCAUAUCGGUCAUACUUUCUUCACGAUAUGGAUUUCACUAAUGAAUAUCCGAAUACUAUGGAUACAACUAUCUCAGAGAUGGGAGGUGGCCUUCGCUGAAAUGCGAUACGAGGAGUGUGGGUAAUGCCGUUAGG ....................(((((((((((((..(((((((..(((((((((....)).)))).......)))..)))).)))....)))).))))))).)).....(((((((..(((..((((...((((((....((((((...........)))))))))))).....((..((((((((.((((((((((((((.(.((((((((((...............))))))))))((((....)))).....).))))))))).........)))))...))))))))..))..((((......)))).....))))...))).)))))))..... (-95.17) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUAACGGCAUUACCCACACUCCUCGUAUCGCAUUUCAGCGAAGGCCACCUCCCAUCUCUGAGAUAGUUGUAUCCAUAGUAUUCGGAUAUUCAUUAGUGAAAUCCAUAUCGUGAAGAAAGUAUGACCGAUAUGGAUAGGAUACUAUGGUCUCAUAUGAGAGGAUACUAUGGUCUAACAUGAGAGGAUACUAUGGUCUCAUAAAAGUUAGAAAUGGAGAAGAGAAAAUGCCGGAUCCCUACCCUGCCACGAACAUUAGAUCGAUCAGAUACGAUAAUCAUGCUUCGGAGAUGAAUCCAAUCGCCUUUUUCAAGCAGAAAGCCGAUAUGUUGUGCGUUUGA .....(((((((.......((((..(((((..(((((((.((.((.......)).)).)))))))........(((((((((((.....((((....))))((((((((((...............)))))))))).)))))))))))((((....)))).))))).....((((((((((((...........))))))....))))))...)))).......)))))))................(((((.....(((.....)))((((((.((((.(....)..)))).....((((.((((((.....)))))).)))).))))))..))))). (-86.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 973 120 71 211 162 NC_002950:PG0807|5end_NusB_family_protein_864724..864954_NEGATIVE 847 190 141 132 83 NC_002950:PG0265|5end_hypothetical_protein_298551..298781_NEGATIVE 830 190 142 155 107 NC_002950:PG1426|5end_hypothetical_protein_1511310..1511540_NEGATIVE 812 190 142 155 107 NC_002950:PG0493|5end_hypothetical_protein_534900..535130_NEGATIVE 613 189 141 231 183 NC_002950:PG1389|5end_DNA-binding_protein,_histone-like_family_1471328..1471558_NEGATIVE 473 125 86 107 60 NC_002950:PG0738|5end_cytidine/deoxycytidylate_deaminase_family_protein_786463..786693_POSITIVE 365 328 281 54 7 NC_002950:PG2006|5end_hypothetical_protein_2094587..2094817_POSITIVE 360 120 74 230 170 NC_002950:PG0447|5end_hypothetical_protein_487278..487508_POSITIVE 356 320 277 58 9 NC_002950:PG2131|5end_60_kDa_protein_2236174..2236404_POSITIVE 352 124 82 196 144 NC_002950:PG0165|5end_heat_shock_protein_15_187807..188037_NEGATIVE 350 327 287 209 169 NC_002950:PG1401|5end_beta-eliminating_lyase_1484778..1485008_NEGATIVE 347 325 281 51 4 NC_002950:PG0476|5end_yngK_protein_518762..518992_NEGATIVE 346 311 276 209 170 NC_002950:PG1676|5end_phosphoenolpyruvate_carboxykinase_1762096..1762326_NEGATIVE 342 310 274 148 103 NC_002950:PG1536|5end_cell_division_protein_FtsX,_putative_1616362..1616592_POSITIVE 338 326 282 81 25 NC_002950:PG1613|5end_glyoxalase_family_protein_1693568..1693798_NEGATIVE 336 320 273 183 129 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 336 327 281 73 25 NC_002950:PG0167|5end_ribosomal_protein_L25_189090..189320_NEGATIVE 334 118 73 95 45 NC_002950:PG0859|5end_hypothetical_protein_917865..918095_POSITIVE 333 119 77 182 125 NC_002950:PG0128|5end_hypothetical_protein_149594..149824_POSITIVE 332 326 284 226 175 NC_002950:PG2112|5end_hypothetical_protein_2221471..2221701_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 774 190 142 99 51 NC_002950:PG0494|3end_hypothetical_protein_535094..535244_NEGATIVE 473 125 86 110 63 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 361 315 273 133 91 NC_002950:PG0800|3end_hypothetical_protein_854719..854869_NEGATIVE 358 58 13 66 15 NC_002950:PG0165|3end_heat_shock_protein_15_187370..187520_NEGATIVE 347 325 281 61 14 NC_002950:PG0477|3end_pantoate--beta-alanine_ligase_518752..518902_NEGATIVE 344 119 71 65 7 NC_002950:PG1638|3end_thioredoxin_family_protein_1718664..1718814_NEGATIVE 342 310 261 102 40 NC_002950:PG1874|3end_hypothetical_protein_1969253..1969403_NEGATIVE 339 129 87 144 98 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 335 328 281 118 63 NC_002950:PG0897|3end_alpha-amylase_family_protein_960868..961018_NEGATIVE 335 320 280 145 108 NC_002950:PG0608|3end_hypothetical_protein_663159..663309_POSITIVE 334 329 281 65 11 NC_002950:PG1593|3end_shikimate_kinase_1672143..1672293_POSITIVE 334 325 285 148 92 NC_002950:PG0934|3end_hypothetical_protein_992414..992564_NEGATIVE 334 118 73 105 55 NC_002950:PG0858|3end_hypothetical_protein_917955..918105_POSITIVE 329 328 286 66 8 NC_002950:PG0003|3end_hypothetical_protein_1919..2069_NEGATIVE 327 126 90 104 61 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 324 98 52 69 14 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 323 124 85 130 81 NC_002950:PG2159|3end_protoporphyrinogen_oxidase_2265874..2266024_POSITIVE 322 130 81 110 50 NC_002950:PG0843|3end_hypothetical_protein_904871..905021_NEGATIVE 319 111 77 59 21 NC_002950:PG0703|3end_cobalamin_(5'-phosphate)_synthase,_putative_759006..759156_POSITIVE 318 110 65 146 91 NC_002950:PG2052|3end_dihydrodipicolinate_synthase_2150585..2150735_POSITIVE