Origin IGS: gccttctccgttatactccttattattttgagagctggctatcgctctgcaaatgtagcaaaaaagcccaaccccgatgccccgaaatctctgctgtttatcccatctgttgcactttgatctactcggtaaagaaatatccatttcccttcgttagtatgcccctaacttagtacctttgcttatgtaatgagtttagataaaacgataaagaccgaggccctttttctggtgatgtcccaaccggtggctaagagtaggggcagatttgtcgtgcctatttctaatctgtgcccaaaatggcaattctatatggtatacagtaatttgacaaccactgc .........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 gcagtggttgtcaaattactgtataccatatagaattgccattttgggcacagattagaaataggcacgacaaatctgcccctactcttagccaccggttgggacatcaccagaaaaagggcctcggtctttatcgttttatctaaactcattacataagcaaaggtactaagttaggggcatactaacgaagggaaatggatatttctttaccgagtagatcaaagtgcaacagatgggataaacagcagagatttcggggcatcggggttgggcttttttgctacatttgcagagcgatagccagctctcaaaataataaggagtataacggagaaggc Mask Tandem Repeat Region ================================================ gccttctccgttatactccttattattttgagagctggctatcgctctgcaaatgtagcaaaaaagcccaaccccgatgccccgaaatctctgctgtttatcccatctgttgcactttgatctactcggtaaagaaatatccatttcccttcgttagtatgcccctaacttagtacctttgcttatgtaatgagtttagataaaacgataaagaccgaggccctttttctggtgatgtcccaaccggtggctaagagtaggggcagatttgtcgtgcctatttctaatctgtgcccaaaatggcaattctatatggtatacagtaatttgacaaccactgc Find is-nt database================================================ Query_seq: PG1695:PG1696|PG1695:PG1696:hypothetical protein:type II DNA modification methyltransferase, putative:->->:1779772..1780112 341 gccttctccgttatactccttattattttgagagctggctatcgctctgcaaatgtagcaaaaaagcccaaccccgatgccccgaaatctctgctgtttatcccatctgttgcactttgatctactcggtaaagaaatatccatttcccttcgttagtatgcccctaacttagtacctttgcttatgtaatgagtttagataaaacgataaagaccgaggccctttttctggtgatgtcccaaccggtggctaagagtaggggcagatttgtcgtgcctatttctaatctgtgcccaaaatggcaattctatatggtatacagtaatttgacaaccactgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1695:PG1696|PG1695:PG1696:hypothetical protein:type II DNA modification methyltransferase, putative:->->:1779772..1780112 341 gccttctccgttatactccttattattttgagagctggctatcgctctgcaaatgtagcaaaaaagcccaaccccgatgccccgaaatctctgctgtttatcccatctgttgcactttgatctactcggtaaagaaatatccatttcccttcgttagtatgcccctaacttagtacctttgcttatgtaatgagtttagataaaacgataaagaccgaggccctttttctggtgatgtcccaaccggtggctaagagtaggggcagatttgtcgtgcctatttctaatctgtgcccaaaatggcaattctatatggtatacagtaatttgacaaccactgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1695:PG1696|PG1695:PG1696:hypothetical protein:type II DNA modification methyltransferase, putative:->->:1779772..1780112 341 gccttctccgttatactccttattattttgagagctggctatcgctctgcaaatgtagcaaaaaagcccaaccccgatgccccgaaatctctgctgtttatcccatctgttgcactttgatctactcggtaaagaaatatccatttcccttcgttagtatgcccctaacttagtacctttgcttatgtaatgagtttagataaaacgataaagaccgaggccctttttctggtgatgtcccaaccggtggctaagagtaggggcagatttgtcgtgcctatttctaatctgtgcccaaaatggcaattctatatggtatacagtaatttgacaaccactgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gccttctccgttatactccttattattttgagagctggctatcgctctgcaaatgtagcaaaaaagcccaaccccgatgccccgaaatctctgctgtttatcccatctgttgcactttgatctactcggtaaagaaatatccatttcccttcgttagtatgcccctaacttagtacctttgcttatgtaatgagtttagataaaacgataaagaccgaggccctttttctggtgatgtcccaaccggtggctaagagtaggggcagatttgtcgtgcctatttctaatctgtgcccaaaatggcaattctatatggtatacagtaatttgacaaccactgc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 13 End: 117 ............ M L L I I L R A G Y R S A N V A K K P N P D A P K S L L F I P S V A L ................................................................................................................................................................................................................................ Protein_Len: 50 Strand: + Start: 190 End: 339 ............................................................................................................................................................................................. M S L D K T I K T E A L F L V M S Q P V A K S R G R F V V P I S N L C P K W Q F Y M V Y S N L T T T .. Protein_Len: 43 Strand: - Start: 199 End: 327 ...................................................................................................................................................................................................... I F R Y L G L G K K Q H H G L R H S L T P A S K D H R N R I Q A W F P L E I H Y V T M .............. Protein_Len: 32 Strand: - Start: 186 End: 281 ......................................................................................................................................................................................... T I L K S L V I F V S A R K R T I D W G T A L L L P L N T T G M ............................................................ Protein_Len: 33 Strand: - Start: 42 End: 140 ......................................... R E A F T A F F G L G S A G F D R S N I G D T A S Q D V R Y L F M ......................................................................................................................................................................................................... Protein_Len: 48 Strand: - Start: 1 End: 144 G E G N Y E K N N Q S S A I A R C I Y C F L G V G I G R F R Q Q K D W R N C K S R S P L S I D M ..................................................................................................................................................................................................... gccttctccgttatactccttattattttgagagctggctatcgctctgcaaatgtagcaaaaaagcccaaccccgatgccccgaaatctctgctgtttatcccatctgttgcactttgatctactcggtaaagaaatatccatttcccttcgttagtatgcccctaacttagtacctttgcttatgtaatgagtttagataaaacgataaagaccgaggccctttttctggtgatgtcccaaccggtggctaagagtaggggcagatttgtcgtgcctatttctaatctgtgcccaaaatggcaattctatatggtatacagtaatttgacaaccactgc 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: 87 Start: 306 End: 335 .................................................................................................................................................................................................................................................................................................................GTTGTCAAATTACTGTATACCATATAGAAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gccttctccgttatactccttattattttgagagctggctatcgctctgcaaatgtagcaaaaaagcccaaccccgatgccccgaaatctctgctgtttatcccatctgttgcactttgatctactcggtaaagaaatatccatttcccttcgttagtatgcccctaacttagtacctttgcttatgtaatgagtttagataaaacgataaagaccgaggccctttttctggtgatgtcccaaccggtggctaagagtaggggcagatttgtcgtgcctatttctaatctgtgcccaaaatggcaattctatatggtatacagtaatttgacaaccactgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1695:PG1696|PG1695:PG1696:hypothetical protein:type II DNA modification methyltransferase, putative:->->:1779772..1780112 341 gccttctccgttatactccttattattttgagagctggctatcgctctgcaaatgtagcaaaaaagcccaaccccgatgccccgaaatctctgctgtttatcccatctgttgcactttgatctactcggtaaagaaatatccatttcccttcgttagtatgcccctaacttagtacctttgcttatgtaatgagtttagataaaacgataaagaccgaggccctttttctggtgatgtcccaaccggtggctaagagtaggggcagatttgtcgtgcctatttctaatctgtgcccaaaatggcaattctatatggtatacagtaatttgacaaccactgc Intra-Species Hit: Count: 1 Min: 1 Max: 341 Len: 341 Subject: NC_002950_PG1695_PG1696|hypothetical protein:type II DNA modification methyltransferase, putative|POSITIVE:POSITIVE|[1779772,1780112]|341 HSP 1 e-value: 0.0 bit: 676.0 Len: 341 Query Start:1 Query End:341 Subject Strand: POSITIVE Subject Start: 1 Subject End: 341 gccttctccgttatactccttattattttgagagctggctatcgctctgcaaatgtagcaaaaaagcccaaccccgatgccccgaaatctctgctgtttatcccatctgttgcactttgatctactcggtaaagaaatatccatttcccttcgttagtatgcccctaacttagtacctttgcttatgtaatgagtttagataaaacgataaagaccgaggccctttttctggtgatgtcccaaccggtggctaagagtaggggcagatttgtcgtgcctatttctaatctgtgcccaaaatggcaattctatatggtatacagtaatttgacaaccactgc gccttctccgttatactccttattattttgagagctggctatcgctctgcaaatgtagcaaaaaagcccaaccccgatgccccgaaatctctgctgtttatcccatctgttgcactttgatctactcggtaaagaaatatccatttcccttcgttagtatgcccctaacttagtacctttgcttatgtaatgagtttagataaaacgataaagaccgaggccctttttctggtgatgtcccaaccggtggctaagagtaggggcagatttgtcgtgcctatttctaatctgtgcccaaaatggcaattctatatggtatacagtaatttgacaaccactgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCUUCUCCGUUAUACUCCUUAUUAUUUUGAGAGCUGGCUAUCGCUCUGCAAAUGUAGCAAAAAAGCCCAACCCCGAUGCCCCGAAAUCUCUGCUGUUUAUCCCAUCUGUUGCACUUUGAUCUACUCGGUAAAGAAAUAUCCAUUUCCCUUCGUUAGUAUGCCCCUAACUUAGUACCUUUGCUUAUGUAAUGAGUUUAGAUAAAACGAUAAAGACCGAGGCCCUUUUUCUGGUGAUGUCCCAACCGGUGGCUAAGAGUAGGGGCAGAUUUGUCGUGCCUAUUUCUAAUCUGUGCCCAAAAUGGCAAUUCUAUAUGGUAUACAGUAAUUUGACAACCACUGC (((..(((((..(((........)))..)).)))..))).........(((...((((....((((..((((...((((.....((((.......))))....)))).))))..))))...))))..(((...(((((....))))).....(((((..((((((((.(((((((((.....((((.(((.....))).))))...((((...(((((((.....)))).)))..))))......))).))))))..))))))))...((((.(((((.............((((......)))).........)))))))))....))))).)))..))) (-69.95) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGUGGUUGUCAAAUUACUGUAUACCAUAUAGAAUUGCCAUUUUGGGCACAGAUUAGAAAUAGGCACGACAAAUCUGCCCCUACUCUUAGCCACCGGUUGGGACAUCACCAGAAAAAGGGCCUCGGUCUUUAUCGUUUUAUCUAAACUCAUUACAUAAGCAAAGGUACUAAGUUAGGGGCAUACUAACGAAGGGAAAUGGAUAUUUCUUUACCGAGUAGAUCAAAGUGCAACAGAUGGGAUAAACAGCAGAGAUUUCGGGGCAUCGGGGUUGGGCUUUUUUGCUACAUUUGCAGAGCGAUAGCCAGCUCUCAAAAUAAUAAGGAGUAUAACGGAGAAGGC (((((((((....)))))))))...((((.(((...(((((((((............))))).)))).........((((((((..(((((..(((..((((.......))))...((((((....))))))...((((.....))))................))).))))).))))))))..))).(....)...)))).....(((((.(((.((((...(((((.((((.((((........................))))...)))).)))))....)))).((((.(((((........)))))))))................))).))))). (-84.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 534 88 42 215 169 NC_002950:PG1866|5end_hypothetical_protein_1964531..1964761_POSITIVE 387 79 35 181 138 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 383 266 223 61 10 NC_002950:PG2200|5end_TPR_domain_protein_2308807..2309037_NEGATIVE 374 80 31 62 17 NC_002950:PG0898|5end_hypothetical_protein_963350..963580_NEGATIVE 372 277 234 94 59 NC_002950:PG0738|5end_cytidine/deoxycytidylate_deaminase_family_protein_786463..786693_POSITIVE 371 278 235 76 27 NC_002950:PG0767|5end_4-alpha-glucanotransferase_820533..820763_NEGATIVE 370 277 231 62 15 NC_002950:PG0691|5end_NifU-related_protein_747469..747699_NEGATIVE 361 267 222 217 176 NC_002950:PG1704|5end_thiol:disulfide_interchange_protein_dsbD,_putative_1792819..1793049_NEGATIVE 357 278 240 121 88 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 355 279 239 39 6 NC_002950:PG1804|5end_V-type_ATP_synthase_subunit_B_1898254..1898484_POSITIVE 354 130 81 62 15 NC_002950:PG1675|5end_hypothetical_protein_1760182..1760412_POSITIVE 353 277 233 167 117 NC_002950:PG0936|5end_xanthine/uracil_permease_family_protein_996451..996681_NEGATIVE 352 278 238 199 151 NC_002950:PG0523|5end_inositol-5-monophosphate_dehydrogenase_568394..568624_NEGATIVE 349 107 67 179 123 NC_002950:PG1382|5end_hypothetical_protein_1461331..1461561_POSITIVE 349 46 1 226 165 NC_002950:PG0498|5end_S-ribosylhomocysteinase_537968..538198_POSITIVE 348 294 255 51 20 NC_002950:PG0349|5end_hydrolase,_haloacid_dehalogenase-like_family_384459..384689_POSITIVE 348 118 73 133 73 NC_002950:PG0026|5end_hypothetical_protein_29234..29464_POSITIVE 346 279 231 86 35 NC_002950:PG0242|5end_conserved_hypothetical_protein_TIGR00096_278960..279190_NEGATIVE 346 274 231 66 22 NC_002950:PG0128|5end_hypothetical_protein_149594..149824_POSITIVE 345 257 216 61 19 NC_002950:PG0335|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_370706..370936_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 452 277 231 90 44 NC_002950:PG1330|3end_large_conductance_mechanosensitive_channel_protein_1410165..1410315_POSITIVE 372 277 234 97 62 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 367 290 244 137 78 NC_002950:PG0554|3end_hypothetical_protein_611661..611811_POSITIVE 353 277 233 146 96 NC_002950:PG0937|3end_hypothetical_protein_996472..996622_NEGATIVE 348 294 255 33 2 NC_002950:PG0348|3end_ATP-dependent_DNA_helicase_RecG_384521..384671_POSITIVE 347 79 32 74 32 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 346 279 231 70 19 NC_002950:PG0243|3end_hypothetical_protein_278976..279126_NEGATIVE 346 274 231 59 15 NC_002950:PG0127|3end_ferrochelatase_149667..149817_POSITIVE 345 257 216 44 2 NC_002950:PG0336|3end_hypothetical_protein_370723..370873_NEGATIVE 344 261 221 55 1 NC_002950:PG1547|3end_hypothetical_protein_1624695..1624845_POSITIVE 336 257 215 97 59 NC_002950:PG2041|3end_hypothetical_protein_2139235..2139385_NEGATIVE 336 130 82 130 74 NC_002950:PG0847|3end_hypothetical_protein_909414..909564_POSITIVE 335 112 71 87 45 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 334 85 41 87 43 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 332 278 231 140 88 NC_002950:PG2142|3end_GTP-binding_protein_Era_2248564..2248714_POSITIVE 332 279 231 67 1 NC_002950:PG2110|3end_thiamine_biosynthesis_protein_ThiC_2219449..2219599_NEGATIVE 332 278 232 59 1 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 331 279 231 125 77 NC_002950:PG0639|3end_signal_peptide_peptidase_SppA,_67K_type_691213..691363_NEGATIVE 329 279 231 97 40 NC_002950:PG2159|3end_protoporphyrinogen_oxidase_2265874..2266024_POSITIVE 326 80 31 98 41 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE