Origin IGS: aaaaataacgggattatatattcgtataaattaggtataatctttgtcttacatttatcaattagaaaactgagcagctttgttcagtttttttattgtgactagttatgtagcaagcattaataattatgcttgcttttaaaaacaaatttatatatatgaatatttatggtcatataattcatatttgttcatttattatgcatccaaatattacatttttgtttcaaagaaatacaagaagatgacggaggaaacggttttcaattcttatatgacaaggtttttggagaaataaattggtttacacattgtcgacaaaagctgaactggtaaaggtaaatagttgacttatagtcaatcgtatgctagtctaatatatgtagtatattggaaatgtaaaggaattttaatatttttacatgttcaataaaaaggaaaaaaggaaaaaaacggagggattattt .........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 aaataatccctccgtttttttccttttttcctttttattgaacatgtaaaaatattaaaattcctttacatttccaatatactacatatattagactagcatacgattgactataagtcaactatttacctttaccagttcagcttttgtcgacaatgtgtaaaccaatttatttctccaaaaaccttgtcatataagaattgaaaaccgtttcctccgtcatcttcttgtatttctttgaaacaaaaatgtaatatttggatgcataataaatgaacaaatatgaattatatgaccataaatattcatatatataaatttgtttttaaaagcaagcataattattaatgcttgctacataactagtcacaataaaaaaactgaacaaagctgctcagttttctaattgataaatgtaagacaaagattatacctaatttatacgaatatataatcccgttattttt Mask Tandem Repeat Region ================================================ aaaaataacgggattatatattcgtataaattaggtataatctttgtcttacatttatcaattagaaaactgagcagctttgttcagtttttttattgtgactagttatgtagcaagcattaataattatgcttgcttttaaaaacaaatttatatatatgaatatttatggtcatataattcatatttgttcatttattatgcatccaaatattacatttttgtttcaaagaaatacaagaagatgacggaggaaacggttttcaattcttatatgacaaggtttttggagaaataaattggtttacacattgtcgacaaaagctgaactggtaaaggtaaatagttgacttatagtcaatcgtatgctagtctaatatatgtagtatattggaaatgtaaaggaattttaatatttttacatgttcaataaaaaggaaaaaaggaaaaaaacggagggattattt Find is-nt database================================================ Query_seq: SSA_0226:SSA_0227|SSA_0226:SSA_0227:60 kDa chaperonin:Collagen-binding surface protein, putative:->->:220710..221176 467 aaaaataacgggattatatattcgtataaattaggtataatctttgtcttacatttatcaattagaaaactgagcagctttgttcagtttttttattgtgactagttatgtagcaagcattaataattatgcttgcttttaaaaacaaatttatatatatgaatatttatggtcatataattcatatttgttcatttattatgcatccaaatattacatttttgtttcaaagaaatacaagaagatgacggaggaaacggttttcaattcttatatgacaaggtttttggagaaataaattggtttacacattgtcgacaaaagctgaactggtaaaggtaaatagttgacttatagtcaatcgtatgctagtctaatatatgtagtatattggaaatgtaaaggaattttaatatttttacatgttcaataaaaaggaaaaaaggaaaaaaacggagggattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0226:SSA_0227|SSA_0226:SSA_0227:60 kDa chaperonin:Collagen-binding surface protein, putative:->->:220710..221176 467 aaaaataacgggattatatattcgtataaattaggtataatctttgtcttacatttatcaattagaaaactgagcagctttgttcagtttttttattgtgactagttatgtagcaagcattaataattatgcttgcttttaaaaacaaatttatatatatgaatatttatggtcatataattcatatttgttcatttattatgcatccaaatattacatttttgtttcaaagaaatacaagaagatgacggaggaaacggttttcaattcttatatgacaaggtttttggagaaataaattggtttacacattgtcgacaaaagctgaactggtaaaggtaaatagttgacttatagtcaatcgtatgctagtctaatatatgtagtatattggaaatgtaaaggaattttaatatttttacatgttcaataaaaaggaaaaaaggaaaaaaacggagggattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0226:SSA_0227|SSA_0226:SSA_0227:60 kDa chaperonin:Collagen-binding surface protein, putative:->->:220710..221176 467 aaaaataacgggattatatattcgtataaattaggtataatctttgtcttacatttatcaattagaaaactgagcagctttgttcagtttttttattgtgactagttatgtagcaagcattaataattatgcttgcttttaaaaacaaatttatatatatgaatatttatggtcatataattcatatttgttcatttattatgcatccaaatattacatttttgtttcaaagaaatacaagaagatgacggaggaaacggttttcaattcttatatgacaaggtttttggagaaataaattggtttacacattgtcgacaaaagctgaactggtaaaggtaaatagttgacttatagtcaatcgtatgctagtctaatatatgtagtatattggaaatgtaaaggaattttaatatttttacatgttcaataaaaaggaaaaaaggaaaaaaacggagggattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaataacgggattatatattcgtataaattaggtataatctttgtcttacatttatcaattagaaaactgagcagctttgttcagtttttttattgtgactagttatgtagcaagcattaataattatgcttgcttttaaaaacaaatttatatatatgaatatttatggtcatataattcatatttgttcatttattatgcatccaaatattacatttttgtttcaaagaaatacaagaagatgacggaggaaacggttttcaattcttatatgacaaggtttttggagaaataaattggtttacacattgtcgacaaaagctgaactggtaaaggtaaatagttgacttatagtcaatcgtatgctagtctaatatatgtagtatattggaaatgtaaaggaattttaatatttttacatgttcaataaaaaggaaaaaaggaaaaaaacggagggattattt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 13 End: 102 ............ M I Y S Y K L G I I F V L H L S I R K L S S F V Q F F Y C D ............................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 41 Strand: + Start: 123 End: 245 .......................................................................................................................... M I M L A F K N K F I Y M N I Y G H I I H I C S F I M H P N I T F L F Q R N T R R .............................................................................................................................................................................................................................. Protein_Len: 49 Strand: + Start: 149 End: 295 .................................................................................................................................................... M Y I Y E Y L W S Y N S Y L F I Y Y A S K Y Y I F V S K K Y K K M T E E T V F N S Y M T R F L E K ............................................................................................................................................................................ Protein_Len: 50 Strand: + Start: 184 End: 333 ....................................................................................................................................................................................... M F V H L L C I Q I L H F C F K E I Q E D D G G N G F Q F L Y D K V F G E I N W F T H C R Q K L N W ...................................................................................................................................... Protein_Len: 32 Strand: - Start: 267 End: 362 .......................................................................................................................................................................................................................................................................... N K Y S L T K P S I F Q N V C Q R C F S F Q Y L Y I T S K Y D M ......................................................................................................... Protein_Len: 34 Strand: - Start: 65 End: 166 ................................................................ F V S C S Q E T K K N H S T I Y C A N I I I S A K L F L N I Y I F M ............................................................................................................................................................................................................................................................................................................. aaaaataacgggattatatattcgtataaattaggtataatctttgtcttacatttatcaattagaaaactgagcagctttgttcagtttttttattgtgactagttatgtagcaagcattaataattatgcttgcttttaaaaacaaatttatatatatgaatatttatggtcatataattcatatttgttcatttattatgcatccaaatattacatttttgtttcaaagaaatacaagaagatgacggaggaaacggttttcaattcttatatgacaaggtttttggagaaataaattggtttacacattgtcgacaaaagctgaactggtaaaggtaaatagttgacttatagtcaatcgtatgctagtctaatatatgtagtatattggaaatgtaaaggaattttaatatttttacatgttcaataaaaaggaaaaaaggaaaaaaacggagggattattt 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: 81 Start: 346 End: 375 .........................................................................................................................................................................................................................................................................................................................................................GTTGACTTATAGTCAATCGTATGCTAGTCT............................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaataacgggattatatattcgtataaattaggtataatctttgtcttacatttatcaattagaaaactgagcagctttgttcagtttttttattgtgactagttatgtagcaagcattaataattatgcttgcttttaaaaacaaatttatatatatgaatatttatggtcatataattcatatttgttcatttattatgcatccaaatattacatttttgtttcaaagaaatacaagaagatgacggaggaaacggttttcaattcttatatgacaaggtttttggagaaataaattggtttacacattgtcgacaaaagctgaactggtaaaggtaaatagttgacttatagtcaatcgtatgctagtctaatatatgtagtatattggaaatgtaaaggaattttaatatttttacatgttcaataaaaaggaaaaaaggaaaaaaacggagggattattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -6.3 Tail_Score: -5.88565 Start: 70 End: 87 Full_Region: TTATCAATTAGAAAA CTGAGCA GCTT TGTTCAG TTTTTTTATTGTGAC .....................................................................CTGAGCAGCTTTGTTCAG............................................................................................................................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 80 HP_score: -8.2 Tail_Score: -4.08064 Start: 113 End: 136 Full_Region: GTGACTAGTTATGTA GCAAGCATTA ATAA TTATGCTTGC TTTTAAAAACAAATT ................................................................................................................GCAAGCATTAATAATTATGCTTGC........................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0226:SSA_0227|SSA_0226:SSA_0227:60 kDa chaperonin:Collagen-binding surface protein, putative:->->:220710..221176 467 aaaaataacgggattatatattcgtataaattaggtataatctttgtcttacatttatcaattagaaaactgagcagctttgttcagtttttttattgtgactagttatgtagcaagcattaataattatgcttgcttttaaaaacaaatttatatatatgaatatttatggtcatataattcatatttgttcatttattatgcatccaaatattacatttttgtttcaaagaaatacaagaagatgacggaggaaacggttttcaattcttatatgacaaggtttttggagaaataaattggtttacacattgtcgacaaaagctgaactggtaaaggtaaatagttgacttatagtcaatcgtatgctagtctaatatatgtagtatattggaaatgtaaaggaattttaatatttttacatgttcaataaaaaggaaaaaaggaaaaaaacggagggattattt Intra-Species Hit: Count: 1 Min: 1 Max: 431 Len: 431 Subject: NC_009009_SSA_0226_SSA_0227|60 kDa chaperonin:Collagen-binding surface protein, putative|POSITIVE:POSITIVE|[220710,221176]|467 HSP 1 e-value: 0.0 bit: 813.0 Len: 431 Query Start:1 Query End:431 Subject Strand: POSITIVE Subject Start: 1 Subject End: 431 aaaaataacgggattatatattcgtataaattaggtataatctttgtcttacatttatcaattagaaaactgagcagctttgttcagnnnnnnnattgtgactagttatgtagcaagcattaataattatgcttgcttttaaaaacaaatttatatatatgaatatttatggtcatataattcatatttgttcatttattatgcatccaaatattacatttttgtttcaaagaaatacaagaagatgacggaggaaacggttttcaattcttatatgacaaggtttttggagaaataaattggtttacacattgtcgacaaaagctgaactggtaaaggtaaatagttgacttatagtcaatcgtatgctagtctaatatatgtagtatattggaaatgtaaaggaattttaatatttttacatgttcaat.................................... aaaaataacgggattatatattcgtataaattaggtataatctttgtcttacatttatcaattagaaaactgagcagctttgttcagtttttttattgtgactagttatgtagcaagcattaataattatgcttgcttttaaaaacaaatttatatatatgaatatttatggtcatataattcatatttgttcatttattatgcatccaaatattacatttttgtttcaaagaaatacaagaagatgacggaggaaacggttttcaattcttatatgacaaggtttttggagaaataaattggtttacacattgtcgacaaaagctgaactggtaaaggtaaatagttgacttatagtcaatcgtatgctagtctaatatatgtagtatattggaaatgtaaaggaattttaatatttttacatgttcaat.................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUAACGGGAUUAUAUAUUCGUAUAAAUUAGGUAUAAUCUUUGUCUUACAUUUAUCAAUUAGAAAACUGAGCAGCUUUGUUCAGUUUUUUUAUUGUGACUAGUUAUGUAGCAAGCAUUAAUAAUUAUGCUUGCUUUUAAAAACAAAUUUAUAUAUAUGAAUAUUUAUGGUCAUAUAAUUCAUAUUUGUUCAUUUAUUAUGCAUCCAAAUAUUACAUUUUUGUUUCAAAGAAAUACAAGAAGAUGACGGAGGAAACGGUUUUCAAUUCUUAUAUGACAAGGUUUUUGGAGAAAUAAAUUGGUUUACACAUUGUCGACAAAAGCUGAACUGGUAAAGGUAAAUAGUUGACUUAUAGUCAAUCGUAUGCUAGUCUAAUAUAUGUAGUAUAUUGGAAAUGUAAAGGAAUUUUAAUAUUUUUACAUGUUCAAU ..........(((((((((...............)))))))))(((((..........((((.((((((((((((......)))))))))))).)))).(((.....((((.((((((((........))))))))......((((.(((((((.((.(((((((..(((((.........)))))..))))))).)).......((((((.(((...((((((...)))))).(((.(((((..(((..(.(....)..)..))).))))).))).....))).))))))...))))))).))))..)))).))))))))....(((((..(((((((((.(..((((((.....))))))..).(((...((((((((((...))))))))))...)))............)))))))))..))))).. (-94.86) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGAACAUGUAAAAAUAUUAAAAUUCCUUUACAUUUCCAAUAUACUACAUAUAUUAGACUAGCAUACGAUUGACUAUAAGUCAACUAUUUACCUUUACCAGUUCAGCUUUUGUCGACAAUGUGUAAACCAAUUUAUUUCUCCAAAAACCUUGUCAUAUAAGAAUUGAAAACCGUUUCCUCCGUCAUCUUCUUGUAUUUCUUUGAAACAAAAAUGUAAUAUUUGGAUGCAUAAUAAAUGAACAAAUAUGAAUUAUAUGACCAUAAAUAUUCAUAUAUAUAAAUUUGUUUUUAAAAGCAAGCAUAAUUAUUAAUGCUUGCUACAUAACUAGUCACAAUAAAAAAACUGAACAAAGCUGCUCAGUUUUCUAAUUGAUAAAUGUAAGACAAAGAUUAUACCUAAUUUAUACGAAUAUAUAAUCCCGUUAUUUUU ((((...(((((((..............)))))))...))))....(((((.(((((((((((.....(.(((((...((((.((((.............))))..))))..))))))..(((((......(((((((.(((((((......(..(((((((((.(((....((.......)))))..)))))))))..)......(((....)))....)))))).)...)))))))((((((((.((...(((((((..........)))))))..)).)))))))).....(((((((((........)))))))))))))).))))))........((((((((.((....)).)))))))).....))))).))))).(((...(((((((....((((....)))).)))))))..)))...... (-68.56) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 360 312 66 25 NC_009009:SSA_0094|5end_Cell_wall_metabolism,_LysM_type_protein,_putative_95345..95575_POSITIVE 268 107 65 196 147 NC_009009:SSA_1180|5end_hypothetical_protein_1208559..1208789_NEGATIVE 261 120 71 91 27 NC_009009:SSA_1424|5end_Hydrolase,_putative_1434479..1434709_NEGATIVE 260 118 71 209 152 NC_009009:SSA_0187|5end_Competence_protein_ComYD,_putative_190350..190580_POSITIVE 258 87 42 201 162 NC_009009:SSA_0926|5end_Histone_acetyltransferase_HPA2,_putative_935465..935695_POSITIVE 253 117 72 203 158 NC_009009:SSA_2099|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2104313..2104543_NEGATIVE 248 274 239 149 116 NC_009009:SSA_1843|5end_Histidine_kinase,_putative_1837491..1837721_NEGATIVE 245 370 323 162 119 NC_009009:SSA_0155|5end_hypothetical_protein_150961..151191_POSITIVE 241 260 218 184 146 NC_009009:SSA_0435|5end_Urocanate_hydratase,_putative_438719..438949_NEGATIVE 240 350 305 228 181 NC_009009:SSA_0356|5end_Dipeptidase,_putative_349259..349489_POSITIVE 238 141 110 195 170 NC_009009:SSA_1302|5end_tRNA_(Guanine-N(1)-)-methyltransferase,_putative_1322484..1322714_NEGATIVE 237 118 71 82 20 NC_009009:SSA_1104|5end_50S_ribosomal_protein_L10,_putative_1124743..1124973_POSITIVE 234 120 73 191 139 NC_009009:SSA_1808|5end_hypothetical_protein_1792209..1792439_NEGATIVE 234 117 71 133 84 NC_009009:SSA_0401|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_398462..398692_POSITIVE 234 415 371 171 124 NC_009009:SSA_0329|5end_Glycerol_uptake_facilitator/aquaporin_protein,_putative_322830..323060_POSITIVE 233 99 66 231 190 NC_009009:SSA_0934|5end_HydD,_putative_943208..943438_POSITIVE 232 100 64 191 159 NC_009009:SSA_0790|5end_hypothetical_protein_773047..773277_POSITIVE 231 256 224 219 187 NC_009009:SSA_1986|5end_Acetyltransferase,_GNAT_family,_putative_1982531..1982761_NEGATIVE 231 138 96 189 147 NC_009009:SSA_1810|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1795396..1795626_NEGATIVE 231 120 74 69 27 NC_009009:SSA_1705|5end_hypothetical_protein_1696853..1697083_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 87 42 150 111 NC_009009:SSA_0925|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_935494..935644_POSITIVE 252 98 67 32 1 NC_009009:SSA_0226|3end_60_kDa_chaperonin_220649..220799_POSITIVE 249 370 323 69 16 NC_009009:SSA_0586|3end_Conserved_uncharacterized_protein_578243..578393_POSITIVE 248 370 323 124 66 NC_009009:SSA_1041|3end_Sugar_ABC_transporter,_permease_protein,_putative_1057434..1057584_POSITIVE 246 88 42 68 33 NC_009009:SSA_1106|3end_IgA-specific_metalloendopeptidase_1131678..1131828_POSITIVE 245 370 323 71 28 NC_009009:SSA_0154|3end_hypothetical_protein_150950..151100_POSITIVE 240 350 305 149 102 NC_009009:SSA_0355|3end_DNA_mismatch_repair_protein,_putative_349260..349410_POSITIVE 239 370 324 151 102 NC_009009:SSA_2258|3end_hypothetical_protein_2253389..2253539_NEGATIVE 235 273 239 151 119 NC_009009:SSA_1844|3end_hypothetical_protein_1837488..1837638_NEGATIVE 235 110 66 109 64 NC_009009:SSA_0663|3end_Acetyltransferase,_putative_648788..648938_POSITIVE 233 108 66 141 93 NC_009009:SSA_2189|3end_hypothetical_protein_2190279..2190429_NEGATIVE 231 264 222 84 38 NC_009009:SSA_0027|3end_Acyl_carrier_protein,_putative_31802..31952_POSITIVE 229 290 250 85 44 NC_009009:SSA_1194|3end_Aspartate-semialdehyde_dehydrogenase,_putative_1220113..1220263_NEGATIVE 229 114 73 86 46 NC_009009:SSA_1002|3end_Alpha-galactosidase,_putative_1003942..1004092_POSITIVE 228 80 39 125 81 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 227 120 75 44 6 NC_009009:SSA_1773|3end_hypothetical_protein_1759535..1759685_NEGATIVE 227 113 71 61 12 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 226 369 321 78 34 NC_009009:SSA_0625|3end_Phosphopantetheine_adenylyltransferase_616182..616332_POSITIVE 225 370 321 143 95 NC_009009:SSA_1724|3end_CBS_domain_protein,_putative_1709897..1710047_NEGATIVE 223 369 323 97 39 NC_009009:SSA_1553|3end_Permease,_putative_1556032..1556182_POSITIVE