Origin IGS: ggtaactcccctttattttttatttttcttattcttatagatttattataaatcttgaaagcgataacaaaaagaccaagaattacacaggcgactgttcactcttggactgtcaaaaaaatctgcccataaggacagaaaaaagtaagaaagtgagcatcgctgctcctaagtccgactgcgcctctggcttgtctcattaagttttagcagaacgtagtttcgcttatgctcaaactgcatctatgcctctaagctctgctcgactctgctagctggcaatcactaagaaattagcggaacgtagacttcgcttgcgttcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagttttagcggaacctagacttcgcttgcgctcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagaggcatagaaaaacccagctatccaaatggttagctgggttaggtttgagctacatcatagttttaga .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctaaaactatgatgtagctcaaacctaacccagctaaccatttggatagctgggtttttctatgcctcttaatgagacaagccgtgggcgcagtcgaatttagaggcattgatgcagactgagcgcaagcgaagtctaggttccgctaaaacttaatgagacaagccgtgggcgcagtcgaatttagaggcattgatgcagactgaacgcaagcgaagtctacgttccgctaatttcttagtgattgccagctagcagagtcgagcagagcttagaggcatagatgcagtttgagcataagcgaaactacgttctgctaaaacttaatgagacaagccagaggcgcagtcggacttaggagcagcgatgctcactttcttacttttttctgtccttatgggcagatttttttgacagtccaagagtgaacagtcgcctgtgtaattcttggtctttttgttatcgctttcaagatttataataaatctataagaataagaaaaataaaaaataaaggggagttacc Mask Tandem Repeat Region ================================================ ggtaactcccctttattttttatttttcttattcttatagatttattataaatcttgaaagcgataacaaaaagaccaagaattacacaggcgactgttcactcttggactgtcaaaaaaatctgcccataaggacagaaaaaagtaagaaagtgagcatcgctgctcctaagtccgactgcgcctctggcttgtctcattaagttttagcagaacgtagtttcgcttatgctcaaactgcatctatgcctctaagctctgctcgactctgctagctggcaatcactaagaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaggcatagaaaaacccagctatccaaatggttagctgggttaggtttgagctacatcatagttttaga Find is-nt database================================================ Query_seq: SSA_2093:SSA_2094|SSA_2093:SSA_2094:PTS system, membrane component, putative:Conserved uncharacterized protein:<-<-:2097553..2098079 527 ggtaactcccctttattttttatttttcttattcttatagatttattataaatcttgaaagcgataacaaaaagaccaagaattacacaggcgactgttcactcttggactgtcaaaaaaatctgcccataaggacagaaaaaagtaagaaagtgagcatcgctgctcctaagtccgactgcgcctctggcttgtctcattaagttttagcagaacgtagtttcgcttatgctcaaactgcatctatgcctctaagctctgctcgactctgctagctggcaatcactaagaaattagcggaacgtagacttcgcttgcgttcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagttttagcggaacctagacttcgcttgcgctcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagaggcatagaaaaacccagctatccaaatggttagctgggttaggtttgagctacatcatagttttaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2093:SSA_2094|SSA_2093:SSA_2094:PTS system, membrane component, putative:Conserved uncharacterized protein:<-<-:2097553..2098079 527 ggtaactcccctttattttttatttttcttattcttatagatttattataaatcttgaaagcgataacaaaaagaccaagaattacacaggcgactgttcactcttggactgtcaaaaaaatctgcccataaggacagaaaaaagtaagaaagtgagcatcgctgctcctaagtccgactgcgcctctggcttgtctcattaagttttagcagaacgtagtttcgcttatgctcaaactgcatctatgcctctaagctctgctcgactctgctagctggcaatcactaagaaattagcggaacgtagacttcgcttgcgttcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagttttagcggaacctagacttcgcttgcgctcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagaggcatagaaaaacccagctatccaaatggttagctgggttaggtttgagctacatcatagttttaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2093:SSA_2094|SSA_2093:SSA_2094:PTS system, membrane component, putative:Conserved uncharacterized protein:<-<-:2097553..2098079 527 ggtaactcccctttattttttatttttcttattcttatagatttattataaatcttgaaagcgataacaaaaagaccaagaattacacaggcgactgttcactcttggactgtcaaaaaaatctgcccataaggacagaaaaaagtaagaaagtgagcatcgctgctcctaagtccgactgcgcctctggcttgtctcattaagttttagcagaacgtagtttcgcttatgctcaaactgcatctatgcctctaagctctgctcgactctgctagctggcaatcactaagaaattagcggaacgtagacttcgcttgcgttcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagttttagcggaacctagacttcgcttgcgctcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagaggcatagaaaaacccagctatccaaatggttagctgggttaggtttgagctacatcatagttttaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtaactcccctttattttttatttttcttattcttatagatttattataaatcttgaaagcgataacaaaaagaccaagaattacacaggcgactgttcactcttggactgtcaaaaaaatctgcccataaggacagaaaaaagtaagaaagtgagcatcgctgctcctaagtccgactgcgcctctggcttgtctcattaagttttagcagaacgtagtttcgcttatgctcaaactgcatctatgcctctaagctctgctcgactctgctagctggcaatcactaagaaattagcggaacgtagacttcgcttgcgttcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagttttagcggaacctagacttcgcttgcgctcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagaggcatagaaaaacccagctatccaaatggttagctgggttaggtttgagctacatcatagttttaga Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 15 End: 200 .............. M F Y F S Y S Y R F I I N L E S D N K K T K N Y T G D C S L L D C Q K N L P I R T E K S K K V S I A A P K S D C A S G L ....................................................................................................................................................................................................................................................................................................................................... Protein_Len: 32 Strand: + Start: 276 End: 371 ................................................................................................................................................................................................................................................................................... M A I T K K L A E R R L R L R S V C I N A S K F D C A H G L S H ............................................................................................................................................................ Protein_Len: 36 Strand: + Start: 418 End: 525 ................................................................................................................................................................................................................................................................................................................................................................................................................................. M P L N S T A P T A C L I K R H R K T Q L S K W L A G L G L S Y I I V L .. Protein_Len: 33 Strand: - Start: 102 End: 200 ..................................................................................................... E Q V T L F I Q G Y P C F F T L F H A D S S R L G V A G R A Q R M ....................................................................................................................................................................................................................................................................................................................................... Protein_Len: 30 Strand: - Start: 49 End: 138 ................................................ L D Q F R Y C F S W S N C L R S N V R P S D F F D A W L S M ..................................................................................................................................................................................................................................................................................................................................................................................................... ggtaactcccctttattttttatttttcttattcttatagatttattataaatcttgaaagcgataacaaaaagaccaagaattacacaggcgactgttcactcttggactgtcaaaaaaatctgcccataaggacagaaaaaagtaagaaagtgagcatcgctgctcctaagtccgactgcgcctctggcttgtctcattaagttttagcagaacgtagtttcgcttatgctcaaactgcatctatgcctctaagctctgctcgactctgctagctggcaatcactaagaaattagcggaacgtagacttcgcttgcgttcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagttttagcggaacctagacttcgcttgcgctcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagaggcatagaaaaacccagctatccaaatggttagctgggttaggtttgagctacatcatagttttaga 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================================================ ggtaactcccctttattttttatttttcttattcttatagatttattataaatcttgaaagcgataacaaaaagaccaagaattacacaggcgactgttcactcttggactgtcaaaaaaatctgcccataaggacagaaaaaagtaagaaagtgagcatcgctgctcctaagtccgactgcgcctctggcttgtctcattaagttttagcagaacgtagtttcgcttatgctcaaactgcatctatgcctctaagctctgctcgactctgctagctggcaatcactaagaaattagcggaacgtagacttcgcttgcgttcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagttttagcggaacctagacttcgcttgcgctcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagaggcatagaaaaacccagctatccaaatggttagctgggttaggtttgagctacatcatagttttaga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 79 HP_score: -3.8 Tail_Score: -5.21236 Start: 74 End: 110 Full_Region: cagatttttttgaca gtccaagagtgaacag tcgc ctgtgtaattcttggtc tttttgttatcgctt .........................................................................gtccaagagtgaacagtcgcctgtgtaattcttggtc................................................................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 95 HP_score: -7.7 Tail_Score: -5.42259 Start: 122 End: 139 Full_Region: actttcttacttttt tctgtcc ttat gggcaga tttttttgacagtcc .........................................................................................................................tctgtccttatgggcaga.................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 95 HP_score: -13.3 Tail_Score: -3.28497 Start: 473 End: 498 Full_Region: AGAGGCATAGAAAAA CCCAGCTATCC AAAT GGTTAGCTGGG TTAGGTTTGAGCTAC ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CCCAGCTATCCAAATGGTTAGCTGGG............................. Find igs database================================================ Query_seq: SSA_2093:SSA_2094|SSA_2093:SSA_2094:PTS system, membrane component, putative:Conserved uncharacterized protein:<-<-:2097553..2098079 527 ggtaactcccctttattttttatttttcttattcttatagatttattataaatcttgaaagcgataacaaaaagaccaagaattacacaggcgactgttcactcttggactgtcaaaaaaatctgcccataaggacagaaaaaagtaagaaagtgagcatcgctgctcctaagtccgactgcgcctctggcttgtctcattaagttttagcagaacgtagtttcgcttatgctcaaactgcatctatgcctctaagctctgctcgactctgctagctggcaatcactaagaaattagcggaacgtagacttcgcttgcgttcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagttttagcggaacctagacttcgcttgcgctcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagaggcatagaaaaacccagctatccaaatggttagctgggttaggtttgagctacatcatagttttaga Intra-Species Hit: Count: 1 Min: 28 Max: 527 Len: 500 Subject: NC_009009_SSA_2093_SSA_2094|PTS system, membrane component, putative:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[2097553,2098079]|527 HSP 1 e-value: 0.0 bit: 950.0 Len: 500 Query Start:28 Query End:527 Subject Strand: POSITIVE Subject Start: 28 Subject End: 527 ...........................cttattcttatagatttattataaatcttgaaagcgataacaaaaagaccaagaattacacaggcgactgttcactcttggactgtcnnnnnnntctgcccataaggacagaaaaaagtaagaaagtgagcatcgctgctcctaagtccgactgcgcctctggcttgtctcattaagttttagcagaacgtagtttcgcttatgctcaaactgcatctatgcctctaagctctgctcgactctgctagctggcaatcactaagaaattagcggaacgtagacttcgcttgcgttcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagttttagcggaacctagacttcgcttgcgctcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagaggcatagaaaaacccagctatccaaatggttagctgggttaggtttgagctacatcatagttttaga ...........................cttattcttatagatttattataaatcttgaaagcgataacaaaaagaccaagaattacacaggcgactgttcactcttggactgtcaaaaaaatctgcccataaggacagaaaaaagtaagaaagtgagcatcgctgctcctaagtccgactgcgcctctggcttgtctcattaagttttagcagaacgtagtttcgcttatgctcaaactgcatctatgcctctaagctctgctcgactctgctagctggcaatcactaagaaattagcggaacgtagacttcgcttgcgttcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagttttagcggaacctagacttcgcttgcgctcagtctgcatcaatgcctctaaattcgactgcgcccacggcttgtctcattaagaggcatagaaaaacccagctatccaaatggttagctgggttaggtttgagctacatcatagttttaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUUCUUAUAGAUUUAUUAUAAAUCUUGAAAGCGAUAACAAAAAGACCAAGAAUUACACAGGCGACUGUUCACUCUUGGACUGUCAAAAAAAUCUGCCCAUAAGGACAGAAAAAAGUAAGAAAGUGAGCAUCGCUGCUCCUAAGUCCGACUGCGCCUCUGGCUUGUCUCAUUAAGUUUUAGCAGAACGUAGUUUCGCUUAUGCUCAAACUGCAUCUAUGCCUCUAAGCUCUGCUCGACUCUGCUAGCUGGCAAUCACUAAGAAAUUAGCGGAACGUAGACUUCGCUUGCGUUCAGUCUGCAUCAAUGCCUCUAAAUUCGACUGCGCCCACGGCUUGUCUCAUUAAGUUUUAGCGGAACCUAGACUUCGCUUGCGCUCAGUCUGCAUCAAUGCCUCUAAAUUCGACUGCGCCCACGGCUUGUCUCAUUAAGAGGCAUAGAAAAACCCAGCUAUCCAAAUGGUUAGCUGGGUUAGGUUUGAGCUACAUCAUAGUUUUAGA .((((((((..(((((((...)))))))...))).)))))...........(((((((....(((((.((((((((.((..(((..........((((.((....)).))))....)))..)).))))))))))))).....(((((..(((((((..(((((((((......))))).....)))).)))))))..))))).(((((((((...(((((((((((.((((..((........)).))))((((.((.((((....)))).))...(((((((.(((..(((...((((((((....)))............((((......((((((......))))))...)))).....))))).)))..)))...))))))).....)))).........(((...(((...)))..)))......)))))))))))..((((((((((.((....)).)))))))))).))))))))).......)))))))... (-152.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAAAACUAUGAUGUAGCUCAAACCUAACCCAGCUAACCAUUUGGAUAGCUGGGUUUUUCUAUGCCUCUUAAUGAGACAAGCCGUGGGCGCAGUCGAAUUUAGAGGCAUUGAUGCAGACUGAGCGCAAGCGAAGUCUAGGUUCCGCUAAAACUUAAUGAGACAAGCCGUGGGCGCAGUCGAAUUUAGAGGCAUUGAUGCAGACUGAACGCAAGCGAAGUCUACGUUCCGCUAAUUUCUUAGUGAUUGCCAGCUAGCAGAGUCGAGCAGAGCUUAGAGGCAUAGAUGCAGUUUGAGCAUAAGCGAAACUACGUUCUGCUAAAACUUAAUGAGACAAGCCAGAGGCGCAGUCGGACUUAGGAGCAGCGAUGCUCACUUUCUUACUUUUUUCUGUCCUUAUGGGCAGAUUUUUUUGACAGUCCAAGAGUGAACAGUCGCCUGUGUAAUUCUUGGUCUUUUUGUUAUCGCUUUCAAGAUUUAUAAUAAAUCUAUAAGAAUAAG ...............((((...((((.((((((((((.((....)).))))))))))..((.((((((((.(((..(((..(((...)))...)))..))).)))))))).))...(((((..((....))..))))).))))..))))...((((....(((..(((...(((...(((..(((.((.((((..((((.(((((...(....)...))))).)))).((((((....))))))..))))...((((((((.((((....(((((...((.(((((...))))).)).)))))....)).))))))))))...)).)))..)))..)))...)))...)))...((((.(((.(((((((..((..............(((((((....)))))))..........((.((((((((..((((....))))...)))))))).))...)).)))))))))).(((((((...))))))).))))..)))) (-165.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 937 110 61 228 179 NC_009009:SSA_2093|5end_PTS_system,_membrane_component,_putative_2097462..2097692_NEGATIVE 493 395 353 187 143 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 409 413 371 208 163 NC_009009:SSA_1308|5end_hypothetical_protein_1326818..1327048_NEGATIVE 385 169 129 71 20 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 378 250 202 62 11 NC_009009:SSA_0605|5end_Methyltransferase_gidB,_putative_593707..593937_NEGATIVE 367 260 211 168 123 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 367 250 203 209 148 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 364 170 125 230 181 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 358 165 121 68 18 NC_009009:SSA_1078|5end_hypothetical_protein_1095742..1095972_POSITIVE 354 164 125 36 5 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 352 177 134 217 173 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 346 189 141 224 168 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 345 410 363 230 184 NC_009009:SSA_1540|5end_hypothetical_protein_1545268..1545498_NEGATIVE 344 409 361 58 7 NC_009009:SSA_1070|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_1088742..1088972_POSITIVE 343 262 221 114 58 NC_009009:SSA_2029|5end_Transposase_and_inactivated_derivatives,_putative_2036028..2036258_NEGATIVE 343 256 211 59 6 NC_009009:SSA_0097|5end_Multi_antimicrobial_extrusion_(MATE)_family_transporter,_putative_98148..98378_POSITIVE 342 200 155 35 3 NC_009009:SSA_1383|5end_Aspartate_aminotransferase,_putative_1401718..1401948_NEGATIVE 342 252 212 146 96 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 341 260 213 158 93 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 341 419 376 227 179 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 596 430 383 50 2 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 426 419 371 142 90 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE 385 169 129 78 27 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 384 347 303 143 97 NC_009009:SSA_0040|3end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_47479..47629_POSITIVE 358 165 121 75 25 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 347 259 211 137 99 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 345 179 132 65 13 NC_009009:SSA_2308|3end_hypothetical_protein_2309893..2310043_NEGATIVE 344 409 361 74 23 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 342 200 155 38 6 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 342 252 212 106 56 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE 339 258 211 146 91 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 336 480 431 114 52 NC_009009:SSA_1357|3end_hypothetical_protein_1372077..1372227_NEGATIVE 333 420 371 134 72 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 332 419 376 74 17 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 330 277 231 69 4 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE 328 426 382 138 84 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 327 252 211 56 14 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 322 485 443 69 11 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 322 169 129 129 74 NC_009009:SSA_1236|3end_Mutator_protein,_putative_1261240..1261390_NEGATIVE 322 160 114 68 10 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE