Origin IGS: caggaaagactatttcggagtaccgagaagagattcagaaacactcctaaaatataaatagagcttaaaaggtatcagatggtagaaatatggtatgctcttctattaaatagtagaacttttctcatttttcgattttctcttgtattacttctggattttatttataatcattataaataaaaagaaagagaaaatttaaatagtggaagaacataaaattgatacgaacttcagtggtcggctgaatatattgcgggcaggggttttaggagccaatgacggcattatttccatagcaggtgtggttattggggtagctagtgcgacggacgatgtctggattatctttctgtctggtttggcggcagtctttgcgggtgccttttct .........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 agaaaaggcacccgcaaagactgccgccaaaccagacagaaagataatccagacatcgtccgtcgcactagctaccccaataaccacacctgctatggaaataatgccgtcattggctcctaaaacccctgcccgcaatatattcagccgaccactgaagttcgtatcaattttatgttcttccactatttaaattttctctttctttttatttataatgattataaataaaatccagaagtaatacaagagaaaatcgaaaaatgagaaaagttctactatttaatagaagagcataccatatttctaccatctgataccttttaagctctatttatattttaggagtgtttctgaatctcttctcggtactccgaaatagtctttcctg Mask Tandem Repeat Region ================================================ caggaaagactatttcggagtaccgagaagagattcagaaacactcctaaaatataaatagagcttaaaaggtatcagatggtagaaatatggtatgctcttctattaaatagtagaacttttctcatttttcgattttctcttgtattacttctggattttatttataatcattataaataaaaagaaagagaaaatttaaatagtggaagaacataaaattgatacgaacttcagtggtcggctgaatatattgcgggcaggggttttaggagccaatgacggcattatttccatagcaggtgtggttattggggtagctagtgcgacggacgatgtctggattatctttctgtctggtttggcggcagtctttgcgggtgccttttct Find is-nt database================================================ Query_seq: SSA_0298:SSA_0299|SSA_0298:SSA_0299:Malate permease, putative:hypothetical protein:->->:292508..292898 391 caggaaagactatttcggagtaccgagaagagattcagaaacactcctaaaatataaatagagcttaaaaggtatcagatggtagaaatatggtatgctcttctattaaatagtagaacttttctcatttttcgattttctcttgtattacttctggattttatttataatcattataaataaaaagaaagagaaaatttaaatagtggaagaacataaaattgatacgaacttcagtggtcggctgaatatattgcgggcaggggttttaggagccaatgacggcattatttccatagcaggtgtggttattggggtagctagtgcgacggacgatgtctggattatctttctgtctggtttggcggcagtctttgcgggtgccttttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0298:SSA_0299|SSA_0298:SSA_0299:Malate permease, putative:hypothetical protein:->->:292508..292898 391 caggaaagactatttcggagtaccgagaagagattcagaaacactcctaaaatataaatagagcttaaaaggtatcagatggtagaaatatggtatgctcttctattaaatagtagaacttttctcatttttcgattttctcttgtattacttctggattttatttataatcattataaataaaaagaaagagaaaatttaaatagtggaagaacataaaattgatacgaacttcagtggtcggctgaatatattgcgggcaggggttttaggagccaatgacggcattatttccatagcaggtgtggttattggggtagctagtgcgacggacgatgtctggattatctttctgtctggtttggcggcagtctttgcgggtgccttttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0298:SSA_0299|SSA_0298:SSA_0299:Malate permease, putative:hypothetical protein:->->:292508..292898 391 caggaaagactatttcggagtaccgagaagagattcagaaacactcctaaaatataaatagagcttaaaaggtatcagatggtagaaatatggtatgctcttctattaaatagtagaacttttctcatttttcgattttctcttgtattacttctggattttatttataatcattataaataaaaagaaagagaaaatttaaatagtggaagaacataaaattgatacgaacttcagtggtcggctgaatatattgcgggcaggggttttaggagccaatgacggcattatttccatagcaggtgtggttattggggtagctagtgcgacggacgatgtctggattatctttctgtctggtttggcggcagtctttgcgggtgccttttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 3 Min: 224 Max: 391 Len: 168 Subject: UniRef90_Q8DV71 Cluster: Hypothetical protein; n=1; Streptococcus mutans|Rep: Hypothetical protein - Streptococcus mutans HSP 1 e-value: 4.0E-10 bit: 65.9 Len: 168 Query Start:224 Query End:391 Subject Strand: null Subject Start: 17 Subject End: 72 ............................................................................................................................................................................................................................... D T N F S G R L N I L R A G V L G A N D X X X X X X X X X X X X X X X T D D V W I I F L S G L A A V F A G A F S ............................................................................................................................................................................................................................... D D N F S G R L N I L R A G V L G A N D G I I S V A G V V I G V A S A T T N I W F I F L S G L S A I L A G A F S Subject: UniRef90_Q03LR1 Cluster: Uncharacterized membrane protein; n=3; Streptococcus thermophilus|Rep: Uncharacterized membrane protein - Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9) HSP 1 e-value: 5.0E-8 bit: 58.9 Len: 168 Query Start:224 Query End:391 Subject Strand: null Subject Start: 3 Subject End: 58 ............................................................................................................................................................................................................................... D T N F S G R L N I L R A G V L G A N D X X X X X X X X X X X X X X X T D D V W I I F L S G L A A V F A G A F S ............................................................................................................................................................................................................................... D K N F A E R L N I L R A G V L G A N D G I I S I A G V V I G V A S A T S N I W F I L I S A L S A I F A G A F S Subject: UniRef90_Q3D077 Cluster: Membrane protein, putative; n=8; Streptococcus agalactiae|Rep: Membrane protein, putative - Streptococcus agalactiae H36B HSP 1 e-value: 4.0E-7 bit: 55.8 Len: 162 Query Start:230 Query End:391 Subject Strand: null Subject Start: 6 Subject End: 59 ..................................................................................................................................................................................................................................... N F S G R L N I L R A G V L G A N D X X X X X X X X X X X X X X X T D D V W I I F L S G L A A V F A G A F S ..................................................................................................................................................................................................................................... N F S Q Q L N I L R A G V L G A N D G I I S V A G V V I G V A S A T H N L W I I F L S A A S A I L A G A F S caggaaagactatttcggagtaccgagaagagattcagaaacactcctaaaatataaatagagcttaaaaggtatcagatggtagaaatatggtatgctcttctattaaatagtagaacttttctcatttttcgattttctcttgtattacttctggattttatttataatcattataaataaaaagaaagagaaaatttaaatagtggaagaacataaaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 58 End: 180 ......................................................... M E L K R Y Q M V E I W Y A L L L N S R T F L I F R F S L V L L L D F I Y N H Y K ................................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 110 End: 199 ............................................................................................................. M V E L F S F F D F L L Y Y F W I L F I I I I N K K K E K I ................................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 203 End: 391 .......................................................................................................................................................................................................... M V E E H K I D T N F S G R L N I L R A G V L G A N D G I I S I A G V V I G V A S A T D D V W I I F L S G L A A V F A G Protein_Len: 49 Strand: - Start: 202 End: 348 ......................................................................................................................................................................................................... I T S S C L I S V F K L P R S F I N R A P T K P A L S P M I E M A P T T I P T A L A V S S T Q I M ........................................... caggaaagactatttcggagtaccgagaagagattcagaaacactcctaaaatataaatagagcttaaaaggtatcagatggtagaaatatggtatgctcttctattaaatagtagaacttttctcatttttcgattttctcttgtattacttctggattttatttataatcattataaataaaaagaaagagaaaatttaaatagtggaagaacataaaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 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: 142 End: 171 .............................................................................................................................................CTTGTATTACTTCTGGATTTTATTTATAAT............................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caggaaagactatttcggagtaccgagaagagattcagaaacactcctaaaatataaatagagcttaaaaggtatcagatggtagaaatatggtatgctcttctattaaatagtagaacttttctcatttttcgattttctcttgtattacttctggattttatttataatcattataaataaaaagaaagagaaaatttaaatagtggaagaacataaaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -2.1 Tail_Score: -3.65522 Start: 294 End: 308 Full_Region: ATGACGGCATTATTT CCATA GCAGG TGTGG TTATTGGGGTAGCTA .....................................................................................................................................................................................................................................................................................................CCATAGCAGGTGTGG................................................................................... Find igs database================================================ Query_seq: SSA_0298:SSA_0299|SSA_0298:SSA_0299:Malate permease, putative:hypothetical protein:->->:292508..292898 391 caggaaagactatttcggagtaccgagaagagattcagaaacactcctaaaatataaatagagcttaaaaggtatcagatggtagaaatatggtatgctcttctattaaatagtagaacttttctcatttttcgattttctcttgtattacttctggattttatttataatcattataaataaaaagaaagagaaaatttaaatagtggaagaacataaaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 223 Len: 223 Subject: NC_009009_SSA_0298_SSA_0299|Malate permease, putative:hypothetical protein|POSITIVE:POSITIVE|[292508,292898]|391 HSP 1 e-value: 1.0E-123 bit: 442.0 Len: 223 Query Start:1 Query End:223 Subject Strand: POSITIVE Subject Start: 1 Subject End: 223 caggaaagactatttcggagtaccgagaagagattcagaaacactcctaaaatataaatagagcttaaaaggtatcagatggtagaaatatggtatgctcttctattaaatagtagaacttttctcatttttcgattttctcttgtattacttctggattttatttataatcattataaataaaaagaaagagaaaatttaaatagtggaagaacataaaatt........................................................................................................................................................................ caggaaagactatttcggagtaccgagaagagattcagaaacactcctaaaatataaatagagcttaaaaggtatcagatggtagaaatatggtatgctcttctattaaatagtagaacttttctcatttttcgattttctcttgtattacttctggattttatttataatcattataaataaaaagaaagagaaaatttaaatagtggaagaacataaaatt........................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGGAAAGACUAUUUCGGAGUACCGAGAAGAGAUUCAGAAACACUCCUAAAAUAUAAAUAGAGCUUAAAAGGUAUCAGAUGGUAGAAAUAUGGUAUGCUCUUCUAUUAAAUAGUAGAACUUUUCUCAUUUUUCGAUUUUCUCUUGUAUUACUUCUGGAUUUUAUUUAUAAUCAUUAUAAAUAAAAAGAAAGAGAAAAUUUAAAUAGUGGAAGAACAUAAAAUU .((((.......((((((....)))))).(.....)........))))...........(((((.......((((((.((.......)).)))))))))))((((((....))))))..(((((.(((((((.(((((((((((......(....)..(((((((((((.....)))))))))))...))))))))))).))).))))))))).......... (-40.01) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUAUGUUCUUCCACUAUUUAAAUUUUCUCUUUCUUUUUAUUUAUAAUGAUUAUAAAUAAAAUCCAGAAGUAAUACAAGAGAAAAUCGAAAAAUGAGAAAAGUUCUACUAUUUAAUAGAAGAGCAUACCAUAUUUCUACCAUCUGAUACCUUUUAAGCUCUAUUUAUAUUUUAGGAGUGUUUCUGAAUCUCUUCUCGGUACUCCGAAAUAGUCUUUCCUG .....((((((((((.....(((..((((((((((((((((((((((((.....)))))))))))...)))........))))))))))..)))....(((.....)))...........))))))))))...........................(((..((((((........((((((...((((........)))))))))).)))))).)))..... (-38.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 46 10 215 175 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 272 38 2 183 141 NC_009009:SSA_0726|5end_FmtA-like_protein,_putative_710905..711135_POSITIVE 256 48 2 190 150 NC_009009:SSA_1515|5end_hypothetical_protein_1522129..1522359_NEGATIVE 250 104 70 205 178 NC_009009:SSA_0661|5end_Isoleucyl-tRNA_synthetase,_putative_644876..645106_POSITIVE 248 48 1 104 50 NC_009009:SSA_2292|5end_DNA_segregation_ATPase_FtsK/SpoIIIE-like_protein,_putative_2294173..2294403_POSITIVE 244 49 2 203 149 NC_009009:SSA_1658|5end_Cationic_amino_acid_transporter,_putative_1654674..1654904_NEGATIVE 241 117 75 114 75 NC_009009:SSA_0589|5end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_580745..580975_POSITIVE 240 27 3 174 143 NC_009009:SSA_1847|5end_RRNA_methyltransferase_RsmB,_putative_1842004..1842234_NEGATIVE 240 177 136 131 85 NC_009009:SSA_1298|5end_Maltose/maltodextrin_ABC_transporter,_sugar-binding_protein_MalX,_putative_1315291..1315521_POSITIVE 238 83 45 217 180 NC_009009:SSA_0961|5end_Possible_ketopantoate_reductase_PanE/ApbA,_putative_969913..970143_POSITIVE 235 49 2 197 150 NC_009009:SSA_2155|5end_hypothetical_protein_2156102..2156332_NEGATIVE 233 155 114 153 106 NC_009009:SSA_0986|5end_Choline_transporter,_putative_988273..988503_POSITIVE 228 52 20 48 4 NC_009009:SSA_1663|5end_Collagen-binding_protein_A_1664121..1664351_NEGATIVE 224 48 3 101 34 NC_009009:SSA_1568|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571200..1571430_POSITIVE 223 153 112 112 75 NC_009009:SSA_0021|5end_hypothetical_protein_26842..27072_POSITIVE 222 85 43 200 151 NC_009009:SSA_1730|5end_hypothetical_protein_1716057..1716287_NEGATIVE 222 49 12 104 54 NC_009009:SSA_1554|5end_hypothetical_protein_1555949..1556179_POSITIVE 222 105 74 194 161 NC_009009:SSA_1332|5end_hypothetical_protein_1347645..1347875_NEGATIVE 221 100 60 141 102 NC_009009:SSA_2340|5end_hypothetical_protein_2342843..2343073_NEGATIVE 221 144 101 158 109 NC_009009:SSA_1611|5end_Era-like_GTP-binding_protein,_putative_1616032..1616262_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 46 10 51 11 NC_009009:SSA_2010|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_2011296..2011446_NEGATIVE 239 48 2 81 36 NC_009009:SSA_0081|3end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_84220..84370_NEGATIVE 236 86 42 67 15 NC_009009:SSA_0938|3end_hypothetical_protein_946945..947095_POSITIVE 235 49 2 83 36 NC_009009:SSA_2156|3end_Conserved_uncharacterized_protein_2156216..2156366_NEGATIVE 233 155 114 139 92 NC_009009:SSA_0985|3end_hypothetical_protein_988339..988489_POSITIVE 224 48 3 88 21 NC_009009:SSA_1567|3end_Polar_amino_acid_ABC_transporter,_amino_acid-binding_protein,_putative_1571267..1571417_POSITIVE 222 49 12 107 57 NC_009009:SSA_1553|3end_Permease,_putative_1556032..1556182_POSITIVE 222 105 74 146 113 NC_009009:SSA_1333|3end_hypothetical_protein_1347693..1347843_NEGATIVE 221 144 101 91 42 NC_009009:SSA_1612|3end_Diacylglycerol_kinase,_putative_1616099..1616249_NEGATIVE 218 142 112 107 74 NC_009009:SSA_2016|3end_Phosphoglycerate_mutase,_putative_2015592..2015742_NEGATIVE 218 150 112 140 95 NC_009009:SSA_1128|3end_Voltage_gated_chloride_channel_EriC,_putative_1154886..1155036_POSITIVE 217 157 113 132 73 NC_009009:SSA_1208|3end_23S_rRNA_pseudouridine_synthase,_putative_1232298..1232448_NEGATIVE 215 96 58 55 18 NC_009009:SSA_2292|3end_DNA_segregation_ATPase_FtsK/SpoIIIE-like_protein,_putative_2295353..2295503_POSITIVE 215 157 111 131 75 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 215 50 1 82 31 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 214 104 74 61 35 NC_009009:SSA_2378|3end_Two-component_system_transcriptional_regulator,_LytR/AlgR_family,_putative_2383129..2383279_NEGATIVE 213 163 121 136 103 NC_009009:SSA_1761|3end_Hemolysin_(containing_CBS_domains),_putative_1747437..1747587_NEGATIVE 212 66 24 88 41 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE 212 47 1 57 13 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 210 159 114 137 92 NC_009009:SSA_0962|3end_Lactoylglutathione_lyase,_putative_971431..971581_POSITIVE