Origin IGS: aaagataagtttcggtttcttaaaatagcatatatgaggaagtagaagcaaatagccgctgcttcttttttgtgccgaatctgcttatcgttcttatctaatagagtgcctttgattcgcagttgcataaagctgtacataactggcctttatgggggagtttttattttttgcacaaatgtgcgaaaaaatttaaataagctaatttgttctataatgtattgacgtactgagataaaggtgatacattctagttacaaacaaaaataaatcactttcaaacaaaagaacaggtttttgttaattataaagataggagcgattgtaacat .........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 atgttacaatcgctcctatctttataattaacaaaaacctgttcttttgtttgaaagtgatttatttttgtttgtaactagaatgtatcacctttatctcagtacgtcaatacattatagaacaaattagcttatttaaattttttcgcacatttgtgcaaaaaataaaaactcccccataaaggccagttatgtacagctttatgcaactgcgaatcaaaggcactctattagataagaacgataagcagattcggcacaaaaaagaagcagcggctatttgcttctacttcctcatatatgctattttaagaaaccgaaacttatcttt Mask Tandem Repeat Region ================================================ aaagataagtttcggtttcttaaaatagcatatatgaggaagtagaagcaaatagccgctgcttcttttttgtgccgaatctgcttatcgttcttatctaatagagtgcctttgattcgcagttgcataaagctgtacataactggcctttatgggggagtttttattttttgcacaaatgtgcgaaaaaatttaaataagctaatttgttctataatgtattgacgtactgagataaaggtgatacattctagttacaaacaaaaataaatcactttcaaacaaaagaacaggtttttgttaattataaagataggagcgattgtaacat Find is-nt database================================================ Query_seq: SSA_0281:SSA_0282|SSA_0281:SSA_0282:hypothetical protein:Phosphotransferase system (PTS), cellobiose-specific IIA component, putative:->->:274024..274354 331 aaagataagtttcggtttcttaaaatagcatatatgaggaagtagaagcaaatagccgctgcttcttttttgtgccgaatctgcttatcgttcttatctaatagagtgcctttgattcgcagttgcataaagctgtacataactggcctttatgggggagtttttattttttgcacaaatgtgcgaaaaaatttaaataagctaatttgttctataatgtattgacgtactgagataaaggtgatacattctagttacaaacaaaaataaatcactttcaaacaaaagaacaggtttttgttaattataaagataggagcgattgtaacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0281:SSA_0282|SSA_0281:SSA_0282:hypothetical protein:Phosphotransferase system (PTS), cellobiose-specific IIA component, putative:->->:274024..274354 331 aaagataagtttcggtttcttaaaatagcatatatgaggaagtagaagcaaatagccgctgcttcttttttgtgccgaatctgcttatcgttcttatctaatagagtgcctttgattcgcagttgcataaagctgtacataactggcctttatgggggagtttttattttttgcacaaatgtgcgaaaaaatttaaataagctaatttgttctataatgtattgacgtactgagataaaggtgatacattctagttacaaacaaaaataaatcactttcaaacaaaagaacaggtttttgttaattataaagataggagcgattgtaacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0281:SSA_0282|SSA_0281:SSA_0282:hypothetical protein:Phosphotransferase system (PTS), cellobiose-specific IIA component, putative:->->:274024..274354 331 aaagataagtttcggtttcttaaaatagcatatatgaggaagtagaagcaaatagccgctgcttcttttttgtgccgaatctgcttatcgttcttatctaatagagtgcctttgattcgcagttgcataaagctgtacataactggcctttatgggggagtttttattttttgcacaaatgtgcgaaaaaatttaaataagctaatttgttctataatgtattgacgtactgagataaaggtgatacattctagttacaaacaaaaataaatcactttcaaacaaaagaacaggtttttgttaattataaagataggagcgattgtaacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagataagtttcggtttcttaaaatagcatatatgaggaagtagaagcaaatagccgctgcttcttttttgtgccgaatctgcttatcgttcttatctaatagagtgcctttgattcgcagttgcataaagctgtacataactggcctttatgggggagtttttattttttgcacaaatgtgcgaaaaaatttaaataagctaatttgttctataatgtattgacgtactgagataaaggtgatacattctagttacaaacaaaaataaatcactttcaaacaaaagaacaggtttttgttaattataaagataggagcgattgtaacat Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 52 End: 222 ................................................... M A A A S F L C R I C L S F L S N R V P L I R S C I K L Y I T G L Y G G V F I F C T N V R K N L N K L I C S I M Y ............................................................................................................. Protein_Len: 31 Strand: - Start: 153 End: 245 ........................................................................................................................................................ P P T K I K Q V F T R F F K F L S I Q E I I Y Q R V S I F T M ...................................................................................... Protein_Len: 32 Strand: - Start: 97 End: 192 ................................................................................................ R I S H R Q N A T A Y L Q V Y S A K I P S N K N K A C I H S F M ........................................................................................................................................... Protein_Len: 46 Strand: - Start: 3 End: 140 .. S L N R N R L I A Y I L F Y F C I A A A E K K H R I Q K D N K D L L T G K I R L Q M F S Y M ............................................................................................................................................................................................... aaagataagtttcggtttcttaaaatagcatatatgaggaagtagaagcaaatagccgctgcttcttttttgtgccgaatctgcttatcgttcttatctaatagagtgcctttgattcgcagttgcataaagctgtacataactggcctttatgggggagtttttattttttgcacaaatgtgcgaaaaaatttaaataagctaatttgttctataatgtattgacgtactgagataaaggtgatacattctagttacaaacaaaaataaatcactttcaaacaaaagaacaggtttttgttaattataaagataggagcgattgtaacat 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================================================ aaagataagtttcggtttcttaaaatagcatatatgaggaagtagaagcaaatagccgctgcttcttttttgtgccgaatctgcttatcgttcttatctaatagagtgcctttgattcgcagttgcataaagctgtacataactggcctttatgggggagtttttattttttgcacaaatgtgcgaaaaaatttaaataagctaatttgttctataatgtattgacgtactgagataaaggtgatacattctagttacaaacaaaaataaatcactttcaaacaaaagaacaggtttttgttaattataaagataggagcgattgtaacat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -2.9 Tail_Score: -5.24531 Start: 39 End: 65 Full_Region: AATAGCATATATGAG GAAGTAGAAGC AAATA GCCGCTGCTTC TTTTTTGTGCCGAAT ......................................GAAGTAGAAGCAAATAGCCGCTGCTTC.......................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 45 HP_score: -3.3 Tail_Score: -2.81256 Start: 45 End: 65 Full_Region: attcggcacaaaaaa gaagcag cggctat ttgcttc tacttcctcatatat ............................................gaagcagcggctatttgcttc.......................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 73 HP_score: -9.0 Tail_Score: -2.79327 Start: 167 End: 190 Full_Region: ATGGGGGAGTTTTTA TTTTTTGCAC AAAT GTGCGAAAAA ATTTAAATAAGCTAA ......................................................................................................................................................................TTTTTTGCACAAATGTGCGAAAAA............................................................................................................................................. Find igs database================================================ Query_seq: SSA_0281:SSA_0282|SSA_0281:SSA_0282:hypothetical protein:Phosphotransferase system (PTS), cellobiose-specific IIA component, putative:->->:274024..274354 331 aaagataagtttcggtttcttaaaatagcatatatgaggaagtagaagcaaatagccgctgcttcttttttgtgccgaatctgcttatcgttcttatctaatagagtgcctttgattcgcagttgcataaagctgtacataactggcctttatgggggagtttttattttttgcacaaatgtgcgaaaaaatttaaataagctaatttgttctataatgtattgacgtactgagataaaggtgatacattctagttacaaacaaaaataaatcactttcaaacaaaagaacaggtttttgttaattataaagataggagcgattgtaacat Intra-Species Hit: Count: 1 Min: 1 Max: 331 Len: 331 Subject: NC_009009_SSA_0281_SSA_0282|hypothetical protein:Phosphotransferase system (PTS), cellobiose-specific IIA component, putative|POSITIVE:POSITIVE|[274024,274354]|331 HSP 1 e-value: 1.0E-166 bit: 585.0 Len: 331 Query Start:1 Query End:331 Subject Strand: POSITIVE Subject Start: 1 Subject End: 331 aaagataagtttcggtttcttaaaatagcatatatgaggaagtagaagcaaatagccgctgcttcttttttgtgccgaatctgcttatcgttcttatctaatagagtgcctttgattcgcagttgcataaagctgtacataactggcctttatgggggagnnnnnnnnnnnngcacaaatgtgcgaaaaaatttaaataagctaatttgttctataatgtattgacgtactgagataaaggtgatacattctagttacaaacaaaaataaatcactttcaaacaaaagaacaggtttttgttaattataaagataggagcgattgtaacat aaagataagtttcggtttcttaaaatagcatatatgaggaagtagaagcaaatagccgctgcttcttttttgtgccgaatctgcttatcgttcttatctaatagagtgcctttgattcgcagttgcataaagctgtacataactggcctttatgggggagtttttattttttgcacaaatgtgcgaaaaaatttaaataagctaatttgttctataatgtattgacgtactgagataaaggtgatacattctagttacaaacaaaaataaatcactttcaaacaaaagaacaggtttttgttaattataaagataggagcgattgtaacat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAUAAGUUUCGGUUUCUUAAAAUAGCAUAUAUGAGGAAGUAGAAGCAAAUAGCCGCUGCUUCUUUUUUGUGCCGAAUCUGCUUAUCGUUCUUAUCUAAUAGAGUGCCUUUGAUUCGCAGUUGCAUAAAGCUGUACAUAACUGGCCUUUAUGGGGGAGUUUUUAUUUUUUGCACAAAUGUGCGAAAAAAUUUAAAUAAGCUAAUUUGUUCUAUAAUGUAUUGACGUACUGAGAUAAAGGUGAUACAUUCUAGUUACAAACAAAAAUAAAUCACUUUCAAACAAAAGAACAGGUUUUUGUUAAUUAUAAAGAUAGGAGCGAUUGUAACAU .(((...((.((((((...........(((.....((((((((((..((.....))..))))))))))..))))))))).)).))).((((((((((((.((((((.(((....((..((((((......))))))..))....)))))))))..(..(((.....((((((((((....))))))))))...............(((((.(((.((((((((..(.............)..)))))))).)))..)))))............)))..).((((((((......))))))))........))))))))))))......... (-84.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUUACAAUCGCUCCUAUCUUUAUAAUUAACAAAAACCUGUUCUUUUGUUUGAAAGUGAUUUAUUUUUGUUUGUAACUAGAAUGUAUCACCUUUAUCUCAGUACGUCAAUACAUUAUAGAACAAAUUAGCUUAUUUAAAUUUUUUCGCACAUUUGUGCAAAAAAUAAAAACUCCCCCAUAAAGGCCAGUUAUGUACAGCUUUAUGCAACUGCGAAUCAAAGGCACUCUAUUAGAUAAGAACGAUAAGCAGAUUCGGCACAAAAAAGAAGCAGCGGCUAUUUGCUUCUACUUCCUCAUAUAUGCUAUUUUAAGAAACCGAAACUUAUCUUU .((((...((((.((.(((((..(((.............((((((..(((((((..(((((.((((((.((.....)).)))))).)))))...(((....)))..)))).)))....)))))).....((((......(((((((.((((....)))))))))))..................((.((((..(((......)))..)))))).......))))....))).))))).)).)))).))))..(((((........((((((((.......))))))))...............((......))...))))).......... (-55.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 99 54 86 28 NC_009009:SSA_0706|5end_RNA_helicase,_putative_691363..691593_POSITIVE 350 95 51 72 29 NC_009009:SSA_0184|5end_Competence_protein_ComYA,_putative_188156..188386_POSITIVE 329 99 58 77 33 NC_009009:SSA_0940|5end_NOL1/NOP2/sun_family_protein,_putative_947626..947856_POSITIVE 325 49 7 199 159 NC_009009:SSA_0863|5end_Cof_family_protein,_putative_855015..855245_NEGATIVE 325 126 81 201 152 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 323 112 73 38 3 NC_009009:SSA_2106|5end_Flavin_monoxygenase,_putative_2109064..2109294_NEGATIVE 319 93 55 211 175 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 312 50 3 200 139 NC_009009:SSA_1796|5end_Transcription_elongation_factor_GreA,_putative_1778307..1778537_NEGATIVE 306 169 129 167 119 NC_009009:SSA_1117|5end_hypothetical_protein_1142743..1142973_POSITIVE 297 65 27 194 164 NC_009009:SSA_1569|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571891..1572121_POSITIVE 297 96 57 141 91 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 292 80 34 166 127 NC_009009:SSA_2063|5end_Aminopeptidase_PepS,_putative_2064857..2065087_NEGATIVE 292 88 52 151 113 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 290 174 131 195 143 NC_009009:SSA_1871|5end_Penicillin-binding_protein_2X,_putative_1868873..1869103_NEGATIVE 290 110 61 184 139 NC_009009:SSA_0954|5end_hypothetical_protein_958024..958254_POSITIVE 290 96 55 72 21 NC_009009:SSA_0524|5end_Microcompartment_protein,_putative_523150..523380_POSITIVE 289 76 38 229 182 NC_009009:SSA_1501|5end_Cytidylate_kinase,_putative_1505772..1506002_NEGATIVE 289 99 54 83 42 NC_009009:SSA_0554|5end_hypothetical_protein_549265..549495_POSITIVE 288 174 133 171 133 NC_009009:SSA_2092|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095975..2096205_NEGATIVE 288 150 106 100 52 NC_009009:SSA_0761|5end_Transcriptional_regulator,_XRE_family,_putative_743877..744107_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 99 58 76 32 NC_009009:SSA_0939|3end_Inositol_monophosphatase_(Mg++_dependent),_putative_947705..947855_POSITIVE 321 85 47 105 57 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 306 169 129 96 48 NC_009009:SSA_1116|3end_hypothetical_protein_1142752..1142902_POSITIVE 292 80 34 144 105 NC_009009:SSA_2064|3end_hypothetical_protein_2064879..2065029_NEGATIVE 289 83 42 51 3 NC_009009:SSA_0922|3end_hypothetical_protein_932225..932375_NEGATIVE 289 99 54 79 38 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 288 174 133 141 103 NC_009009:SSA_2093|3end_PTS_system,_membrane_component,_putative_2096005..2096155_NEGATIVE 286 148 104 66 21 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 286 177 131 124 66 NC_009009:SSA_0022|3end_Surface_protein_cell_wall_anchor,_sortase_B_family,_putative_28428..28578_POSITIVE 283 158 115 86 45 NC_009009:SSA_0537|3end_Propanediol_utilization:dioldehydratase_reactivation,_putative_533893..534043_POSITIVE 281 126 81 91 37 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 275 93 51 78 32 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 274 94 52 150 113 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 271 75 34 76 35 NC_009009:SSA_1640|3end_hypothetical_protein_1642108..1642258_NEGATIVE 271 78 36 99 59 NC_009009:SSA_0901|3end_Alpha-acetolactate_decarboxylase,_putative_893246..893396_POSITIVE 266 82 41 119 59 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 266 145 102 137 102 NC_009009:SSA_0140|3end_Copper-translocating_P-type_ATPase,_putative_136952..137102_POSITIVE 264 89 47 147 101 NC_009009:SSA_2047|3end_hypothetical_protein_2049735..2049885_NEGATIVE 263 95 56 53 16 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 263 89 57 150 107 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE