Origin IGS: aagtaaaagagaagcagagtaggcttgctgacttgcacagagagtgctgatggctgagagcagcaccaagaaagcaaaagccgaagaacatgtttcgtaatcttttgtgtgattaagcacaaacgtcgctcacgttacgagttcagaggctgccttttagggcggcgaataacagtggtaccacggctttcgtctgttttagagacggaagctttttattttgcagtaggtccagtgaagacgatggggaaatatagctaatatcctgaacagcagggtggagctacgaattgatttgagagggaaagaac .........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 gttctttccctctcaaatcaattcgtagctccaccctgctgttcaggatattagctatatttccccatcgtcttcactggacctactgcaaaataaaaagcttccgtctctaaaacagacgaaagccgtggtaccactgttattcgccgccctaaaaggcagcctctgaactcgtaacgtgagcgacgtttgtgcttaatcacacaaaagattacgaaacatgttcttcggcttttgctttcttggtgctgctctcagccatcagcactctctgtgcaagtcagcaagcctactctgcttctcttttactt Mask Tandem Repeat Region ================================================ aagtaaaagagaagcagagtaggcttgctgacttgcacagagagtgctgatggctgagagcagcaccaagaaagcaaaagccgaagaacatgtttcgtaatcttttgtgtgattaagcacaaacgtcgctcacgttacgagttcagaggctgccttttagggcggcgaataacagtggtaccacggctttcgtctgttttagagacggaagctttttattttgcagtaggtccagtgaagacgatggggaaatatagctaatatcctgaacagcagggtggagctacgaattgatttgagagggaaagaac Find is-nt database================================================ Query_seq: SSA_0567:SSA_0568|SSA_0567:SSA_0568:Isochorismitase family protein, putative:Aspartyl-tRNA synthetase 1, putative:->->:561503..561813 311 aagtaaaagagaagcagagtaggcttgctgacttgcacagagagtgctgatggctgagagcagcaccaagaaagcaaaagccgaagaacatgtttcgtaatcttttgtgtgattaagcacaaacgtcgctcacgttacgagttcagaggctgccttttagggcggcgaataacagtggtaccacggctttcgtctgttttagagacggaagctttttattttgcagtaggtccagtgaagacgatggggaaatatagctaatatcctgaacagcagggtggagctacgaattgatttgagagggaaagaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0567:SSA_0568|SSA_0567:SSA_0568:Isochorismitase family protein, putative:Aspartyl-tRNA synthetase 1, putative:->->:561503..561813 311 aagtaaaagagaagcagagtaggcttgctgacttgcacagagagtgctgatggctgagagcagcaccaagaaagcaaaagccgaagaacatgtttcgtaatcttttgtgtgattaagcacaaacgtcgctcacgttacgagttcagaggctgccttttagggcggcgaataacagtggtaccacggctttcgtctgttttagagacggaagctttttattttgcagtaggtccagtgaagacgatggggaaatatagctaatatcctgaacagcagggtggagctacgaattgatttgagagggaaagaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0567:SSA_0568|SSA_0567:SSA_0568:Isochorismitase family protein, putative:Aspartyl-tRNA synthetase 1, putative:->->:561503..561813 311 aagtaaaagagaagcagagtaggcttgctgacttgcacagagagtgctgatggctgagagcagcaccaagaaagcaaaagccgaagaacatgtttcgtaatcttttgtgtgattaagcacaaacgtcgctcacgttacgagttcagaggctgccttttagggcggcgaataacagtggtaccacggctttcgtctgttttagagacggaagctttttattttgcagtaggtccagtgaagacgatggggaaatatagctaatatcctgaacagcagggtggagctacgaattgatttgagagggaaagaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtaaaagagaagcagagtaggcttgctgacttgcacagagagtgctgatggctgagagcagcaccaagaaagcaaaagccgaagaacatgtttcgtaatcttttgtgtgattaagcacaaacgtcgctcacgttacgagttcagaggctgccttttagggcggcgaataacagtggtaccacggctttcgtctgttttagagacggaagctttttattttgcagtaggtccagtgaagacgatggggaaatatagctaatatcctgaacagcagggtggagctacgaattgatttgagagggaaagaac Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 150 End: 254 ..................................................................................................................................................... M P F R A A N N S G T T A F V C F R D G S F L F C S R S S E D D G E I ......................................................... Protein_Len: 53 Strand: + Start: 100 End: 258 ................................................................................................... M F C V I K H K R R S R Y E F R G C L L G R R I T V V P R L S S V L E T E A F Y F A V G P V K T M G K Y S ..................................................... Protein_Len: 30 Strand: - Start: 202 End: 291 ......................................................................................................................................................................................................... L R F S K I K C Y T W H L R H P F I A L I R F L L T S S R M .................... Protein_Len: 39 Strand: - Start: 146 End: 262 ................................................................................................................................................. L S G K L A A F L L P V V A K T Q K L S P L K K N Q L L D L S S S P S I Y S M ................................................. Protein_Len: 40 Strand: - Start: 3 End: 122 .. Y F L L L T P K S V Q V S L A S P Q S C C W S L L L R L V H K T I K Q T I L C M ............................................................................................................................................................................................. Protein_Len: 30 Strand: - Start: 2 End: 91 . T F S F C L L S A S K C L S H Q H S L A A G L F C F G F F M ............................................................................................................................................................................................................................ Protein_Len: 40 Strand: - Start: 1 End: 120 L L L S A S Y A Q Q S A C L T S I A S L L V L F A F A S S C T E Y D K T H N L M ............................................................................................................................................................................................... aagtaaaagagaagcagagtaggcttgctgacttgcacagagagtgctgatggctgagagcagcaccaagaaagcaaaagccgaagaacatgtttcgtaatcttttgtgtgattaagcacaaacgtcgctcacgttacgagttcagaggctgccttttagggcggcgaataacagtggtaccacggctttcgtctgttttagagacggaagctttttattttgcagtaggtccagtgaagacgatggggaaatatagctaatatcctgaacagcagggtggagctacgaattgatttgagagggaaagaac 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================================================ aagtaaaagagaagcagagtaggcttgctgacttgcacagagagtgctgatggctgagagcagcaccaagaaagcaaaagccgaagaacatgtttcgtaatcttttgtgtgattaagcacaaacgtcgctcacgttacgagttcagaggctgccttttagggcggcgaataacagtggtaccacggctttcgtctgttttagagacggaagctttttattttgcagtaggtccagtgaagacgatggggaaatatagctaatatcctgaacagcagggtggagctacgaattgatttgagagggaaagaac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.2 Tail_Score: -5.46706 Start: 186 End: 212 Full_Region: AACAGTGGTACCACG GCTTTCGTCTGT TTT AGAGACGGAAGC TTTTTATTTTGCAGT .........................................................................................................................................................................................GCTTTCGTCTGTTTTAGAGACGGAAGC................................................................................................... Find igs database================================================ Query_seq: SSA_0567:SSA_0568|SSA_0567:SSA_0568:Isochorismitase family protein, putative:Aspartyl-tRNA synthetase 1, putative:->->:561503..561813 311 aagtaaaagagaagcagagtaggcttgctgacttgcacagagagtgctgatggctgagagcagcaccaagaaagcaaaagccgaagaacatgtttcgtaatcttttgtgtgattaagcacaaacgtcgctcacgttacgagttcagaggctgccttttagggcggcgaataacagtggtaccacggctttcgtctgttttagagacggaagctttttattttgcagtaggtccagtgaagacgatggggaaatatagctaatatcctgaacagcagggtggagctacgaattgatttgagagggaaagaac Intra-Species Hit: Count: 1 Min: 1 Max: 311 Len: 311 Subject: NC_009009_SSA_0567_SSA_0568|Isochorismitase family protein, putative:Aspartyl-tRNA synthetase 1, putative|POSITIVE:POSITIVE|[561503,561813]|311 HSP 1 e-value: 1.0E-175 bit: 617.0 Len: 311 Query Start:1 Query End:311 Subject Strand: POSITIVE Subject Start: 1 Subject End: 311 aagtaaaagagaagcagagtaggcttgctgacttgcacagagagtgctgatggctgagagcagcaccaagaaagcaaaagccgaagaacatgtttcgtaatcttttgtgtgattaagcacaaacgtcgctcacgttacgagttcagaggctgccttttagggcggcgaataacagtggtaccacggctttcgtctgttttagagacggaagctttttattttgcagtaggtccagtgaagacgatggggaaatatagctaatatcctgaacagcagggtggagctacgaattgatttgagagggaaagaac aagtaaaagagaagcagagtaggcttgctgacttgcacagagagtgctgatggctgagagcagcaccaagaaagcaaaagccgaagaacatgtttcgtaatcttttgtgtgattaagcacaaacgtcgctcacgttacgagttcagaggctgccttttagggcggcgaataacagtggtaccacggctttcgtctgttttagagacggaagctttttattttgcagtaggtccagtgaagacgatggggaaatatagctaatatcctgaacagcagggtggagctacgaattgatttgagagggaaagaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAAAAGAGAAGCAGAGUAGGCUUGCUGACUUGCACAGAGAGUGCUGAUGGCUGAGAGCAGCACCAAGAAAGCAAAAGCCGAAGAACAUGUUUCGUAAUCUUUUGUGUGAUUAAGCACAAACGUCGCUCACGUUACGAGUUCAGAGGCUGCCUUUUAGGGCGGCGAAUAACAGUGGUACCACGGCUUUCGUCUGUUUUAGAGACGGAAGCUUUUUAUUUUGCAGUAGGUCCAGUGAAGACGAUGGGGAAAUAUAGCUAAUAUCCUGAACAGCAGGGUGGAGCUACGAAUUGAUUUGAGAGGGAAAGAAC ..........((((((.....((((((((..(((((((.....)))).....((((....))))...)))..))))..))))........))))))....((((((((((......)))))..(.((.((((((((............(((((((....)))))))......((.(((.((((((((((((((((.......)))))))))))............)).)))))).))..)))).))))......(((((..(((((((.....))))))).))))).............)).).))))).. (-92.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUCUUUCCCUCUCAAAUCAAUUCGUAGCUCCACCCUGCUGUUCAGGAUAUUAGCUAUAUUUCCCCAUCGUCUUCACUGGACCUACUGCAAAAUAAAAAGCUUCCGUCUCUAAAACAGACGAAAGCCGUGGUACCACUGUUAUUCGCCGCCCUAAAAGGCAGCCUCUGAACUCGUAACGUGAGCGACGUUUGUGCUUAAUCACACAAAAGAUUACGAAACAUGUUCUUCGGCUUUUGCUUUCUUGGUGCUGCUCUCAGCCAUCAGCACUCUCUGUGCAAGUCAGCAAGCCUACUCUGCUUCUCUUUUACUU .....................((((((((((.((..(((.(((((((....((((..............((((.....)))).................((((.(((((.......))))).)))).(((....))).))))...((.(((......))).)).)))))))..)))..))))))....((((((........))))))....))))))...........((((..((((..((.(((((((....))).)))).((((.....)))).))..))))))))..................... (-69.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 447 168 122 104 51 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 435 70 21 206 150 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 411 250 203 186 136 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 379 90 44 223 173 NC_009009:SSA_0513|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_511558..511788_POSITIVE 368 60 14 77 24 NC_009009:SSA_2204|5end_hypothetical_protein_2204663..2204893_POSITIVE 362 210 161 216 162 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 362 168 124 225 172 NC_009009:SSA_0293|5end_hypothetical_protein_287613..287843_NEGATIVE 358 86 46 134 82 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 357 90 47 41 5 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 352 165 128 169 133 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 351 166 126 143 101 NC_009009:SSA_2042|5end_hypothetical_protein_2047073..2047303_NEGATIVE 351 70 21 59 5 NC_009009:SSA_0493|5end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_492868..493098_POSITIVE 349 66 22 191 145 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 349 179 131 206 150 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 347 59 13 72 30 NC_009009:SSA_1078|5end_hypothetical_protein_1095742..1095972_POSITIVE 345 167 125 150 84 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 344 70 21 223 165 NC_009009:SSA_1419|5end_hypothetical_protein_1429675..1429905_NEGATIVE 343 179 138 159 111 NC_009009:SSA_0125|5end_50S_ribosomal_protein_L30,_putative_116930..117160_POSITIVE 342 170 124 53 14 NC_009009:SSA_0412|5end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_408163..408393_NEGATIVE 339 168 124 52 7 NC_009009:SSA_2139|5end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2140324..2140554_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 447 168 122 131 78 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 362 168 124 66 13 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 357 90 47 44 8 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 351 166 126 150 108 NC_009009:SSA_2044|3end_Cysteinyl-tRNA_synthetase,_putative_2047066..2047216_NEGATIVE 347 259 211 125 86 NC_009009:SSA_1569|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1572630..1572780_POSITIVE 347 59 13 79 37 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 343 179 138 145 97 NC_009009:SSA_0124|3end_30S_ribosomal_protein_S5,_putative_116996..117146_POSITIVE 339 168 124 68 23 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE 324 65 21 136 74 NC_009009:SSA_1052|3end_hypothetical_protein_1066846..1066996_NEGATIVE 324 166 121 140 75 NC_009009:SSA_0143|3end_Conserved_uncharacterized_protein_137880..138030_POSITIVE 323 49 3 80 30 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 319 65 21 143 97 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE 317 56 11 128 66 NC_009009:SSA_1933|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase,_putative_1920893..1921043_NEGATIVE 315 65 28 114 62 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 314 166 124 41 3 NC_009009:SSA_2259|3end_hypothetical_protein_2254727..2254877_NEGATIVE 314 208 162 151 87 NC_009009:SSA_1522|3end_Cell_division_protein_FtsW,_putative_1530730..1530880_NEGATIVE 314 57 17 148 106 NC_009009:SSA_1322|3end_Glycosyl_transferase,_putative_1338536..1338686_NEGATIVE 313 168 122 47 4 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 311 216 174 47 6 NC_009009:SSA_0092|3end_V-type_sodium_ATPase,_subunit_B,_putative_94369..94519_POSITIVE 310 65 22 139 100 NC_009009:SSA_1386|3end_NADPH-dependent_FMN_reductase,_putative_1403428..1403578_POSITIVE