Origin IGS: gtctacctcctaaaattatacacagtgtccaaatttcaataaaattgattatacaccaatcgaaaaattattacaagtttattattttaaaactggacaccgtgtctaattttgtttgaaaagattgctgggaagtggagtaagttcgccctactgtctttaatctctgaacaatctgtaaataaaaggtattcttccataggtagggacacagaaaatcagttttatgttagaatgccaaggtttattaccaatcctatgaatctggcggttttgaagttcaaattcctcaatttaaaggatatacccaagaaaaagtcaaaagtattctcggcgaaccagaaaaaataagcaccgacctcgcatctgaaagcaaagcacttgaagaaaagaattagaaaatcttaaaagactgattcaggagcaaaaaataagtaccgaacaagcgcgtgctttctta .........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 taagaaagcacgcgcttgttcggtacttattttttgctcctgaatcagtcttttaagattttctaattcttttcttcaagtgctttgctttcagatgcgaggtcggtgcttattttttctggttcgccgagaatacttttgactttttcttgggtatatcctttaaattgaggaatttgaacttcaaaaccgccagattcataggattggtaataaaccttggcattctaacataaaactgattttctgtgtccctacctatggaagaataccttttatttacagattgttcagagattaaagacagtagggcgaacttactccacttcccagcaatcttttcaaacaaaattagacacggtgtccagttttaaaataataaacttgtaataatttttcgattggtgtataatcaattttattgaaatttggacactgtgtataattttaggaggtagac Mask Tandem Repeat Region ================================================ gtctacctcctaaaattatacacagtgtccaaatttcaataaaattgattatacaccaatcgaaaaattattacaagtttattattttaaaactggacaccgtgtctaattttgtttgaaaagattgctgggaagtggagtaagttcgccctactgtctttaatctctgaacaatctgtaaataaaaggtattcttccataggtagggacacagaaaatcagttttatgttagaatgccaaggtttattaccaatcctatgaatctggcggttttgaagttcaaattcctcaatttaaaggatatacccaagaaaaagtcaaaagtattctcggcgaaccagaaaaaataagcaccgacctcgcatctgaaagcaaagcacttgaagaaaagaattagaaaatcttaaaagactgattcaggagcaaaaaataagtaccgaacaagcgcgtgctttctta Find is-nt database================================================ Query_seq: SSA_2343:SSA_2344|SSA_2343:SSA_2344:hypothetical protein:hypothetical protein:<-->:2346217..2346676 460 gtctacctcctaaaattatacacagtgtccaaatttcaataaaattgattatacaccaatcgaaaaattattacaagtttattattttaaaactggacaccgtgtctaattttgtttgaaaagattgctgggaagtggagtaagttcgccctactgtctttaatctctgaacaatctgtaaataaaaggtattcttccataggtagggacacagaaaatcagttttatgttagaatgccaaggtttattaccaatcctatgaatctggcggttttgaagttcaaattcctcaatttaaaggatatacccaagaaaaagtcaaaagtattctcggcgaaccagaaaaaataagcaccgacctcgcatctgaaagcaaagcacttgaagaaaagaattagaaaatcttaaaagactgattcaggagcaaaaaataagtaccgaacaagcgcgtgctttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2343:SSA_2344|SSA_2343:SSA_2344:hypothetical protein:hypothetical protein:<-->:2346217..2346676 460 gtctacctcctaaaattatacacagtgtccaaatttcaataaaattgattatacaccaatcgaaaaattattacaagtttattattttaaaactggacaccgtgtctaattttgtttgaaaagattgctgggaagtggagtaagttcgccctactgtctttaatctctgaacaatctgtaaataaaaggtattcttccataggtagggacacagaaaatcagttttatgttagaatgccaaggtttattaccaatcctatgaatctggcggttttgaagttcaaattcctcaatttaaaggatatacccaagaaaaagtcaaaagtattctcggcgaaccagaaaaaataagcaccgacctcgcatctgaaagcaaagcacttgaagaaaagaattagaaaatcttaaaagactgattcaggagcaaaaaataagtaccgaacaagcgcgtgctttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2343:SSA_2344|SSA_2343:SSA_2344:hypothetical protein:hypothetical protein:<-->:2346217..2346676 460 gtctacctcctaaaattatacacagtgtccaaatttcaataaaattgattatacaccaatcgaaaaattattacaagtttattattttaaaactggacaccgtgtctaattttgtttgaaaagattgctgggaagtggagtaagttcgccctactgtctttaatctctgaacaatctgtaaataaaaggtattcttccataggtagggacacagaaaatcagttttatgttagaatgccaaggtttattaccaatcctatgaatctggcggttttgaagttcaaattcctcaatttaaaggatatacccaagaaaaagtcaaaagtattctcggcgaaccagaaaaaataagcaccgacctcgcatctgaaagcaaagcacttgaagaaaagaattagaaaatcttaaaagactgattcaggagcaaaaaataagtaccgaacaagcgcgtgctttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 234 Max: 457 Len: 224 Subject: UniRef90_Q8DRZ2 Cluster: Hypothetical protein; n=1; Streptococcus mutans|Rep: Hypothetical protein - Streptococcus mutans HSP 1 e-value: 6.0E-10 bit: 58.9 Len: 159 Query Start:234 Query End:392 Subject Strand: null Subject Start: 92 Subject End: 143 ......................................................................................................................................................................................................................................... N A K V Y Y Q S Y E S G G F E V Q I P Q F K G Y T Q E K V K S I L G E P E K I S T D L A S E S K A L E E K .................................................................... ......................................................................................................................................................................................................................................... D A K V Y Y - S N E N D G F E A Q I S D F K G Y N Q D K V K K I L G K P D S I S T D Q N A I Q N G F K E K .................................................................... HSP 2 e-value: 6.0E-10 bit: 26.6 Len: 69 Query Start:389 Query End:457 Subject Strand: null Subject Start: 143 Subject End: 165 .................................................................................................................................................................................................................................................................................................................................................................................................... K E L E N L K R L I Q E Q K I S T E Q A R A F ... .................................................................................................................................................................................................................................................................................................................................................................................................... K E L E N I N E L I N S G S L T E E Q G K A F ... gtctacctcctaaaattatacacagtgtccaaatttcaataaaattgattatacaccaatcgaaaaattattacaagtttattattttaaaactggacaccgtgtctaattttgtttgaaaagattgctgggaagtggagtaagttcgccctactgtctttaatctctgaacaatctgtaaataaaaggtattcttccataggtagggacacagaaaatcagttttatgttagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 15 End: 116 .............. M I H S V Q I S I K L I I H Q S K N Y Y K F I I L K L D T V S N F V ........................................................................................................................................................................................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 109 End: 348 ............................................................................................................ M L F E K I A G K W S K F A L L S L I S E Q S V N K R Y S S I G R D T E N Q F Y V R M P R F I T N P M N L A V L K F K F ................................................................................................................ Protein_Len: 37 Strand: + Start: 285 End: 395 ............................................................................................................................................................................................................................................................................................ M P Q F K G Y T Q E K V K S I L G E P E K I S T D L A S E S K A L E E K N ................................................................. Protein_Len: 32 Strand: - Start: 322 End: 417 ................................................................................................................................................................................................................................................................................................................................. F Y E R R V L F F L C R G R M Q F C L V Q L F S N S F R L L S M ........................................... Protein_Len: 56 Strand: - Start: 228 End: 395 ................................................................................................................................................................................................................................... T L I G L N I V L G I F R A T K F N L N R L K F S I G L F F D F T N E A F W F F Y A G V E C R F A F C K F F L M ................................................................. Protein_Len: 44 Strand: - Start: 163 End: 294 .................................................................................................................................................................. D R F L R Y I F P I R G Y T P V C F I L K I N S H W P K N G I R H I Q R N Q L E F E E M ...................................................................................................................................................................... Protein_Len: 41 Strand: - Start: 90 End: 212 ......................................................................................... F Q V G H R I K N S F I A P F H L L N A R S D K I E S C D T F L L Y E E M P L S M ........................................................................................................................................................................................................................................................ Protein_Len: 47 Strand: - Start: 74 End: 214 ......................................................................... L N I I K F S S V T D L K T Q F S Q Q S T S Y T R G V T K L R Q V I Q L Y F T N K W L Y P C M ...................................................................................................................................................................................................................................................... gtctacctcctaaaattatacacagtgtccaaatttcaataaaattgattatacaccaatcgaaaaattattacaagtttattattttaaaactggacaccgtgtctaattttgtttgaaaagattgctgggaagtggagtaagttcgccctactgtctttaatctctgaacaatctgtaaataaaaggtattcttccataggtagggacacagaaaatcagttttatgttagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntta 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: 88 Start: 48 End: 77 ...............................................CTTGTAATAATTTTTCGATTGGTGTATAAT............................................................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 15 End: 44 ..............TTTTATTGAAATTTGGACACTGTGTATAAT................................................................................................................................................................................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtctacctcctaaaattatacacagtgtccaaatttcaataaaattgattatacaccaatcgaaaaattattacaagtttattattttaaaactggacaccgtgtctaattttgtttgaaaagattgctgggaagtggagtaagttcgccctactgtctttaatctctgaacaatctgtaaataaaaggtattcttccataggtagggacacagaaaatcagttttatgttagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2343:SSA_2344|SSA_2343:SSA_2344:hypothetical protein:hypothetical protein:<-->:2346217..2346676 460 gtctacctcctaaaattatacacagtgtccaaatttcaataaaattgattatacaccaatcgaaaaattattacaagtttattattttaaaactggacaccgtgtctaattttgtttgaaaagattgctgggaagtggagtaagttcgccctactgtctttaatctctgaacaatctgtaaataaaaggtattcttccataggtagggacacagaaaatcagttttatgttagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntta Intra-Species Hit: Count: 1 Min: 1 Max: 232 Len: 232 Subject: NC_009009_SSA_2343_SSA_2344|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2346217,2346676]|460 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 gtctacctcctaaaattatacacagtgtccaaatttcaataaaattgattatacaccaatcgaaaaattattacaagtttattattttaaaactggacaccgtgtctaattttgtttgaaaagattgctgggaagtggagtaagttcgccctactgtctttaatctctgaacaatctgtaaataaaaggtattcttccataggtagggacacagaaaatcagttttatgtta.................................................................................................................................................................................................................................... gtctacctcctaaaattatacacagtgtccaaatttcaataaaattgattatacaccaatcgaaaaattattacaagtttattattttaaaactggacaccgtgtctaattttgtttgaaaagattgctgggaagtggagtaagttcgccctactgtctttaatctctgaacaatctgtaaataaaaggtattcttccataggtagggacacagaaaatcagttttatgtta.................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUACCUCCUAAAAUUAUACACAGUGUCCAAAUUUCAAUAAAAUUGAUUAUACACCAAUCGAAAAAUUAUUACAAGUUUAUUAUUUUAAAACUGGACACCGUGUCUAAUUUUGUUUGAAAAGAUUGCUGGGAAGUGGAGUAAGUUCGCCCUACUGUCUUUAAUCUCUGAACAAUCUGUAAAUAAAAGGUAUUCUUCCAUAGGUAGGGACACAGAAAAUCAGUUUUAUGUUA (((..(((((((..((((.((((.(((((((.............((((((.......))))))..............((((......))))..))))))).)))).))))((((((((...((((((.(.(((..(((((..(((.......)))..)))))...))).).)))))).)))))))).............)))).))))))...................... (-46.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAUAAAACUGAUUUUCUGUGUCCCUACCUAUGGAAGAAUACCUUUUAUUUACAGAUUGUUCAGAGAUUAAAGACAGUAGGGCGAACUUACUCCACUUCCCAGCAAUCUUUUCAAACAAAAUUAGACACGGUGUCCAGUUUUAAAAUAAUAAACUUGUAAUAAUUUUUCGAUUGGUGUAUAAUCAAUUUUAUUGAAAUUUGGACACUGUGUAUAAUUUUAGGAGGUAGAC ..(((((.((......)).)))))..((((((..(((((.....((((.((((...((....))..)))).))))..((((((.....))))))...))))).................(((((((.(((((((((((((((((((.((((.....))))...........(((((((.....)))))))...)))))).))))))))))))).)))))))...)))))).. (-53.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 884 140 91 231 182 NC_009009:SSA_2343|5end_hypothetical_protein_2346126..2346356_NEGATIVE 332 158 111 187 136 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 296 178 135 224 177 NC_009009:SSA_1794|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1777049..1777279_NEGATIVE 294 158 120 150 116 NC_009009:SSA_0589|5end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_580745..580975_POSITIVE 291 169 122 62 7 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 291 170 121 175 133 NC_009009:SSA_0903|5end_NAD(P)H_dehydrogenase_(quinone),_putative_893242..893472_POSITIVE 288 170 123 202 151 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 285 168 122 206 149 NC_009009:SSA_1229|5end_hypothetical_protein_1252421..1252651_NEGATIVE 281 209 165 57 8 NC_009009:SSA_1510|5end_Rhamnosyltransferase,_putative_1515336..1515566_NEGATIVE 281 152 114 203 158 NC_009009:SSA_0350|5end_Helicase,_putative_344218..344448_NEGATIVE 281 163 125 120 66 NC_009009:SSA_0203|5end_hypothetical_protein_201322..201552_POSITIVE 276 148 103 147 104 NC_009009:SSA_0715|5end_DNA_uptake_protein,_putative_700726..700956_POSITIVE 261 159 121 161 121 NC_009009:SSA_0533|5end_Glycerol_dehydratase_large_subunit_pduC,_putative_528970..529200_POSITIVE 259 170 121 215 164 NC_009009:SSA_0548|5end_Alanine_racemase,_putative_542340..542570_POSITIVE 257 136 98 150 101 NC_009009:SSA_1860|5end_Penicillin-binding_protein_1A,_putative_1854299..1854529_POSITIVE 257 170 123 192 143 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 253 167 130 152 115 NC_009009:SSA_1828|5end_Glycerol_uptake_facilitator_protein,_putative_1818007..1818237_POSITIVE 253 225 188 48 5 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 252 169 123 224 169 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 250 168 121 206 151 NC_009009:SSA_0389|5end_hypothetical_protein_384172..384402_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 158 111 136 85 NC_009009:SSA_0806|3end_hypothetical_protein_789478..789628_POSITIVE 294 223 201 95 72 NC_009009:SSA_1993|3end_Conserved_uncharacterized_protein_1990380..1990530_NEGATIVE 291 170 121 99 57 NC_009009:SSA_0901|3end_Alpha-acetolactate_decarboxylase,_putative_893246..893396_POSITIVE 290 158 127 32 3 NC_009009:SSA_0588|3end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_580707..580857_POSITIVE 281 152 114 143 98 NC_009009:SSA_0351|3end_Signal_peptidase_I,_putative_344278..344428_NEGATIVE 281 163 125 120 66 NC_009009:SSA_0202|3end_hypothetical_protein_201402..201552_POSITIVE 269 158 117 79 41 NC_009009:SSA_1877|3end_hypothetical_protein_1871915..1872065_POSITIVE 261 159 121 139 99 NC_009009:SSA_0532|3end_Propanediol_utilization_protein_PduB,_putative_529028..529178_POSITIVE 259 155 111 70 11 NC_009009:SSA_0227|3end_Collagen-binding_surface_protein,_putative_222970..223120_POSITIVE 254 229 186 53 12 NC_009009:SSA_0850|3end_Ubiquitin_C-terminal_hydrolase,_putative_837641..837791_POSITIVE 253 167 130 83 46 NC_009009:SSA_1827|3end_Alpha-glycerophosphate_oxidase,_putative_1818018..1818168_POSITIVE 247 170 128 106 54 NC_009009:SSA_2022|3end_Transcriptional_regulator,_MerR_family_(multidrug-efflux_transporter_genes),_putative_2024488..2024638_POSITIVE 244 169 123 115 53 NC_009009:SSA_0495|3end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_496036..496186_POSITIVE 237 160 123 149 96 NC_009009:SSA_1476|3end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1482448..1482598_POSITIVE 237 157 111 67 3 NC_009009:SSA_0636|3end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625809..625959_POSITIVE 236 152 125 69 42 NC_009009:SSA_0262|3end_ABC-type_Mn/Zn_transporter,_ATP-ase_component,_putative_255455..255605_NEGATIVE 234 157 122 51 17 NC_009009:SSA_2017|3end_Hypothetical_protein_(possibly_membrane-associated)_2016435..2016585_NEGATIVE 234 163 128 46 6 NC_009009:SSA_1949|3end_AliA_protein,_putative_1942403..1942553_NEGATIVE 234 177 141 104 69 NC_009009:SSA_1595|3end_Tellurite_resistance,_putative_1600951..1601101_NEGATIVE 234 169 126 149 102 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE