Origin IGS: cagtttctcctttgtatattaattgataaaatatttatcgcatatttagtatactattctcttgctatggttgcaagcgtttccaaaatctcttctgctagctaaaatgaataaattcccctaggaaaaaattactctagctgtatacctagcagcccctccaaacctgttgtataaatttccatagatgtatatcaagctgtataaaaatttttttgtaaaagaaaaaagccagataaaatctgactttaaagacacgtggctgcggaggcacaaaccgcagccgcgcaagtattgcaggaaagaatggataggagaaaaagaacaaacttatctcctattaccaaattggttgtacttcatagcttagattattttaccgtcttctctagacaagcaatc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattgcttgtctagagaagacggtaaaataatctaagctatgaagtacaaccaatttggtaataggagataagtttgttctttttctcctatccattctttcctgcaatacttgcgcggctgcggtttgtgcctccgcagccacgtgtctttaaagtcagattttatctggcttttttcttttacaaaaaaatttttatacagcttgatatacatctatggaaatttatacaacaggtttggaggggctgctaggtatacagctagagtaattttttcctaggggaatttattcattttagctagcagaagagattttggaaacgcttgcaaccatagcaagagaatagtatactaaatatgcgataaatattttatcaattaatatacaaaggagaaactg Mask Tandem Repeat Region ================================================ cagtttctcctttgtatattaattgataaaatatttatcgcatatttagtatactattctcttgctatggttgcaagcgtttccaaaatctcttctgctagctaaaatgaataaattcccctaggaaaaaattactctagctgtatacctagcagcccctccaaacctgttgtataaatttccatagatgtatatcaagctgtataaaaatttttttgtaaaagaaaaaagccagataaaatctgactttaaagacacgtggctgcggaggcacaaaccgcagccgcgcaagtattgcaggaaagaatggataggagaaaaagaacaaacttatctcctattaccaaattggttgtacttcatagcttagattattttaccgtcttctctagacaagcaatc Find is-nt database================================================ Query_seq: SSA_1593:SSA_1594|SSA_1593:SSA_1594:Dipeptidase, putative:Metalloendopeptidase, putative:<-<-:1598145..1598546 402 cagtttctcctttgtatattaattgataaaatatttatcgcatatttagtatactattctcttgctatggttgcaagcgtttccaaaatctcttctgctagctaaaatgaataaattcccctaggaaaaaattactctagctgtatacctagcagcccctccaaacctgttgtataaatttccatagatgtatatcaagctgtataaaaatttttttgtaaaagaaaaaagccagataaaatctgactttaaagacacgtggctgcggaggcacaaaccgcagccgcgcaagtattgcaggaaagaatggataggagaaaaagaacaaacttatctcctattaccaaattggttgtacttcatagcttagattattttaccgtcttctctagacaagcaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1593:SSA_1594|SSA_1593:SSA_1594:Dipeptidase, putative:Metalloendopeptidase, putative:<-<-:1598145..1598546 402 cagtttctcctttgtatattaattgataaaatatttatcgcatatttagtatactattctcttgctatggttgcaagcgtttccaaaatctcttctgctagctaaaatgaataaattcccctaggaaaaaattactctagctgtatacctagcagcccctccaaacctgttgtataaatttccatagatgtatatcaagctgtataaaaatttttttgtaaaagaaaaaagccagataaaatctgactttaaagacacgtggctgcggaggcacaaaccgcagccgcgcaagtattgcaggaaagaatggataggagaaaaagaacaaacttatctcctattaccaaattggttgtacttcatagcttagattattttaccgtcttctctagacaagcaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1593:SSA_1594|SSA_1593:SSA_1594:Dipeptidase, putative:Metalloendopeptidase, putative:<-<-:1598145..1598546 402 cagtttctcctttgtatattaattgataaaatatttatcgcatatttagtatactattctcttgctatggttgcaagcgtttccaaaatctcttctgctagctaaaatgaataaattcccctaggaaaaaattactctagctgtatacctagcagcccctccaaacctgttgtataaatttccatagatgtatatcaagctgtataaaaatttttttgtaaaagaaaaaagccagataaaatctgactttaaagacacgtggctgcggaggcacaaaccgcagccgcgcaagtattgcaggaaagaatggataggagaaaaagaacaaacttatctcctattaccaaattggttgtacttcatagcttagattattttaccgtcttctctagacaagcaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagtttctcctttgtatattaattgataaaatatttatcgcatatttagtatactattctcttgctatggttgcaagcgtttccaaaatctcttctgctagctaaaatgaataaattcccctaggaaaaaattactctagctgtatacctagcagcccctccaaacctgttgtataaatttccatagatgtatatcaagctgtataaaaatttttttgtaaaagaaaaaagccagataaaatctgactttaaagacacgtggctgcggaggcacaaaccgcagccgcgcaagtattgcaggaaagaatggataggagaaaaagaacaaacttatctcctattaccaaattggttgtacttcatagcttagattattttaccgtcttctctagacaagcaatc Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 188 End: 367 ........................................................................................................................................................................................... M Y I K L Y K N F F V K E K S Q I K S D F K D T W L R R H K P Q P R K Y C R K E W I G E K E Q T Y L L L P N W L Y F I A ................................... Protein_Len: 48 Strand: + Start: 259 End: 402 .................................................................................................................................................................................................................................................................. M A A E A Q T A A A Q V L Q E R M D R R K R T N L S P I T K L V V L H S L D Y F T V F S R Q A I Protein_Len: 32 Strand: - Start: 252 End: 347 ........................................................................................................................................................................................................................................................... L C T A A S A C V A A A C T N C S L I S L L F L V F K D G I V M ....................................................... Protein_Len: 60 Strand: - Start: 152 End: 334 ....................................................................................................................................................... G R W V Q Q I F K W L H I D L Q I F I K K Y F F F A L Y F R V K F V R P Q P P V F R L R A L I A P F F P Y S F F F L S M .................................................................... Protein_Len: 60 Strand: - Start: 124 End: 312 ........................................................................................................................... V R A T Y R A A G G F R N Y L N G Y I Y I L S Y L F K K T F S F L W I F D S K L S V H S R L C L G C G R L Y Q L F S H M .......................................................................................... cagtttctcctttgtatattaattgataaaatatttatcgcatatttagtatactattctcttgctatggttgcaagcgtttccaaaatctcttctgctagctaaaatgaataaattcccctaggaaaaaattactctagctgtatacctagcagcccctccaaacctgttgtataaatttccatagatgtatatcaagctgtataaaaatttttttgtaaaagaaaaaagccagataaaatctgactttaaagacacgtggctgcggaggcacaaaccgcagccgcgcaagtattgcaggaaagaatggataggagaaaaagaacaaacttatctcctattaccaaattggttgtacttcatagcttagattattttaccgtcttctctagacaagcaatc 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: 85 Start: 79 End: 108 ..............................................................................GTTTCCAAAATCTCTTCTGCTAGCTAAAAT...................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 48 End: 77 ...............................................CTTGCAACCATAGCAAGAGAATAGTATACT..................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cagtttctcctttgtatattaattgataaaatatttatcgcatatttagtatactattctcttgctatggttgcaagcgtttccaaaatctcttctgctagctaaaatgaataaattcccctaggaaaaaattactctagctgtatacctagcagcccctccaaacctgttgtataaatttccatagatgtatatcaagctgtataaaaatttttttgtaaaagaaaaaagccagataaaatctgactttaaagacacgtggctgcggaggcacaaaccgcagccgcgcaagtattgcaggaaagaatggataggagaaaaagaacaaacttatctcctattaccaaattggttgtacttcatagcttagattattttaccgtcttctctagacaagcaatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -7.3 Tail_Score: -5.79595 Start: 231 End: 247 Full_Region: ccacgtgtctttaaa gtcagat ttt atctggc ttttttcttttacaa ......................................................................................................................................................................................................................................gtcagattttatctggc........................................................................................................................................................... TransTerm Strand: - Conf: 75 HP_score: -8.5 Tail_Score: -3.38224 Start: 256 End: 290 Full_Region: ctttcctgcaatact tgcgcggctgcgg tttgtgcct ccgcagccacgtg tctttaaagtcagat ...............................................................................................................................................................................................................................................................tgcgcggctgcggtttgtgcctccgcagccacgtg................................................................................................................ TransTerm Strand: - Conf: 86 HP_score: -11.1 Tail_Score: -3.26031 Start: 258 End: 288 Full_Region: ttcctgcaatacttg cgcggctgcgg tttgtgcct ccgcagccacg tgtctttaaagtcag .................................................................................................................................................................................................................................................................cgcggctgcggtttgtgcctccgcagccacg.................................................................................................................. TransTerm Strand: - Conf: 41 HP_score: -2.5 Tail_Score: -2.72559 Start: 312 End: 340 Full_Region: caaccaatttggtaa taggagataag tttgttc tttttctccta tccattctttcctgc .......................................................................................................................................................................................................................................................................................................................taggagataagtttgttctttttctccta.............................................................. Find igs database================================================ Query_seq: SSA_1593:SSA_1594|SSA_1593:SSA_1594:Dipeptidase, putative:Metalloendopeptidase, putative:<-<-:1598145..1598546 402 cagtttctcctttgtatattaattgataaaatatttatcgcatatttagtatactattctcttgctatggttgcaagcgtttccaaaatctcttctgctagctaaaatgaataaattcccctaggaaaaaattactctagctgtatacctagcagcccctccaaacctgttgtataaatttccatagatgtatatcaagctgtataaaaatttttttgtaaaagaaaaaagccagataaaatctgactttaaagacacgtggctgcggaggcacaaaccgcagccgcgcaagtattgcaggaaagaatggataggagaaaaagaacaaacttatctcctattaccaaattggttgtacttcatagcttagattattttaccgtcttctctagacaagcaatc Intra-Species Hit: Count: 1 Min: 1 Max: 402 Len: 402 Subject: NC_009009_SSA_1593_SSA_1594|Dipeptidase, putative:Metalloendopeptidase, putative|NEGATIVE:NEGATIVE|[1598145,1598546]|402 HSP 1 e-value: 0.0 bit: 755.0 Len: 402 Query Start:1 Query End:402 Subject Strand: POSITIVE Subject Start: 1 Subject End: 402 cagtttctcctttgtatattaattgataaaatatttatcgcatatttagtatactattctcttgctatggttgcaagcgtttccaaaatctcttctgctagctaaaatgaataaattcccctaggaaaaaattactctagctgtatacctagcagcccctccaaacctgttgtataaatttccatagatgtatatcaagctgtataaaaannnnnnngtaaaagaaaaaagccagataaaatctgactttaaagacacgtggctgcggaggcacaaaccgcagccgcgcaagtattgcaggaaagaatggataggagaaaaagaacaaacttatctcctattaccaaattggttgtacttcatagcttagattattttaccgtcttctctagacaagcaatc cagtttctcctttgtatattaattgataaaatatttatcgcatatttagtatactattctcttgctatggttgcaagcgtttccaaaatctcttctgctagctaaaatgaataaattcccctaggaaaaaattactctagctgtatacctagcagcccctccaaacctgttgtataaatttccatagatgtatatcaagctgtataaaaatttttttgtaaaagaaaaaagccagataaaatctgactttaaagacacgtggctgcggaggcacaaaccgcagccgcgcaagtattgcaggaaagaatggataggagaaaaagaacaaacttatctcctattaccaaattggttgtacttcatagcttagattattttaccgtcttctctagacaagcaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUUUCUCCUUUGUAUAUUAAUUGAUAAAAUAUUUAUCGCAUAUUUAGUAUACUAUUCUCUUGCUAUGGUUGCAAGCGUUUCCAAAAUCUCUUCUGCUAGCUAAAAUGAAUAAAUUCCCCUAGGAAAAAAUUACUCUAGCUGUAUACCUAGCAGCCCCUCCAAACCUGUUGUAUAAAUUUCCAUAGAUGUAUAUCAAGCUGUAUAAAAAUUUUUUUGUAAAAGAAAAAAGCCAGAUAAAAUCUGACUUUAAAGACACGUGGCUGCGGAGGCACAAACCGCAGCCGCGCAAGUAUUGCAGGAAAGAAUGGAUAGGAGAAAAAGAACAAACUUAUCUCCUAUUACCAAAUUGGUUGUACUUCAUAGCUUAGAUUAUUUUACCGUCUUCUCUAGACAAGCAAUC .............(((((((((.((((((.....)))))).....))))))))).....(((.(((((((.(((((.((...........(((((((((((..............((((....)))).....(((.......)))...)))))))..........(((((.((((.........(((((...((((..(((.(((((((....))))))).........)))..))))..)))))............(((((((((((.........)))))))))))...)))).))))).)))).(((((((((((..(((......))).))))))))..)))...)).)))))..)))))))..)))..........((((.....))))........ (-94.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUGCUUGUCUAGAGAAGACGGUAAAAUAAUCUAAGCUAUGAAGUACAACCAAUUUGGUAAUAGGAGAUAAGUUUGUUCUUUUUCUCCUAUCCAUUCUUUCCUGCAAUACUUGCGCGGCUGCGGUUUGUGCCUCCGCAGCCACGUGUCUUUAAAGUCAGAUUUUAUCUGGCUUUUUUCUUUUACAAAAAAAUUUUUAUACAGCUUGAUAUACAUCUAUGGAAAUUUAUACAACAGGUUUGGAGGGGCUGCUAGGUAUACAGCUAGAGUAAUUUUUUCCUAGGGGAAUUUAUUCAUUUUAGCUAGCAGAAGAGAUUUUGGAAACGCUUGCAACCAUAGCAAGAGAAUAGUAUACUAAAUAUGCGAUAAAUAUUUUAUCAAUUAAUAUACAAAGGAGAAACUG ..((.(((((((.....))))(((((((((.(((..((((((((((...(((.....)))..(((((((.(((......)))..)))))))((((.(((((.((((.(((((((.((((((..........((((((.((((..(((.....((((((((((...)))))))))).......)))....(((((((((((......(((....))))))))))))))........)))))))))))))))))))))))..((((((((((((...((((....))))...))).))))))))).)))).)))))...))))...)))).....))))))...)))...(((((.....)))))......)))))))))............))).))...... (-103.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 880 110 61 201 152 NC_009009:SSA_1593|5end_Dipeptidase,_putative_1598054..1598284_NEGATIVE 373 300 254 69 5 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 372 296 258 226 180 NC_009009:SSA_1443|5end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1446672..1446902_NEGATIVE 368 297 253 213 163 NC_009009:SSA_1632|5end_Surface_protein,_putative_1634045..1634275_NEGATIVE 353 290 241 51 2 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 352 289 258 79 49 NC_009009:SSA_1996|5end_DNA-directed_RNA_polymerase_delta_subunit,_putative_1994024..1994254_NEGATIVE 350 309 262 77 16 NC_009009:SSA_1976|5end_Conserved_uncharacterized_protein_1972158..1972388_NEGATIVE 335 297 257 78 30 NC_009009:SSA_0808|5end_hypothetical_protein_790771..791001_POSITIVE 333 289 245 224 172 NC_009009:SSA_2000|5end_hypothetical_protein_1997469..1997699_NEGATIVE 332 310 261 185 115 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 330 307 262 63 14 NC_009009:SSA_0004|5end_Lipoprotein,_putative_3704..3934_NEGATIVE 329 294 253 52 13 NC_009009:SSA_0491|5end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_490961..491191_POSITIVE 326 290 242 53 10 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 323 298 254 94 41 NC_009009:SSA_2331|5end_D-alanine_transfer_protein,_putative_2334964..2335194_NEGATIVE 322 294 258 162 117 NC_009009:SSA_2080|5end_hypothetical_protein_2085341..2085571_NEGATIVE 317 299 254 193 145 NC_009009:SSA_0106|5end_30S_ribosomal_protein_S10,_putative_107772..108002_POSITIVE 316 170 141 34 5 NC_009009:SSA_0805|5end_Collagen-binding_surface_protein,_putative_787476..787706_POSITIVE 316 305 262 50 8 NC_009009:SSA_0086|5end_V-type_sodium_ATPase,_subunit_K,_putative_87839..88069_POSITIVE 315 290 242 61 10 NC_009009:SSA_1454|5end_hypothetical_protein_1461100..1461330_NEGATIVE 313 305 262 75 28 NC_009009:SSA_2056|5end_Cinnamoyl_ester_hydrolase,_putative_2058587..2058817_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 292 253 147 102 NC_009009:SSA_1633|3end_FimA_fimbrial_subunit-like_protein,_putative_1634106..1634256_NEGATIVE 335 297 257 66 18 NC_009009:SSA_0807|3end_GTP-binding_protein,_putative_790839..790989_POSITIVE 329 294 253 55 16 NC_009009:SSA_0490|3end_Cobalamin_5'-phosphate_synthase,_putative_491044..491194_POSITIVE 323 298 254 101 48 NC_009009:SSA_2332|3end_D-alanyl_carrier_protein,_putative_2334957..2335107_NEGATIVE 318 89 47 51 7 NC_009009:SSA_2087|3end_Conserved_uncharacterized_protein_2091674..2091824_NEGATIVE 311 289 241 150 84 NC_009009:SSA_0980|3end_3-isopropylmalate_dehydratase_large_subunit,_putative_985466..985616_POSITIVE 309 103 63 125 83 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 308 303 266 143 103 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 308 290 243 63 1 NC_009009:SSA_0189|3end_Competence_protein_ComGF,_putative_191523..191673_POSITIVE 306 298 259 70 25 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 300 301 264 83 44 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 300 300 261 36 2 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 299 292 258 150 107 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 296 300 253 61 16 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 294 288 242 74 15 NC_009009:SSA_0110|3end_50S_ribosomal_protein_L2,_putative_110666..110816_POSITIVE 290 293 253 144 103 NC_009009:SSA_2064|3end_hypothetical_protein_2064879..2065029_NEGATIVE 290 103 61 117 74 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 288 302 262 151 104 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 287 103 61 134 76 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 286 284 244 72 28 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE