Origin IGS: atttcatctctgttcccttaaggggcagagattttttactccaaccccggattagcagtagtcgctttttagaaagcaaaaaaagaatgtttttttacaatcagtcactatcttgtattcttttgttaatccagactgtgatgttccgtaatatagttgttttaaaataaaaagcaactaagatgtttcctagaacaaattagttgctcagaactacggggaaggccgcttggatatgcaagcgtgaagtacatcaaaacttgatatatataatctttcttaattcctaaatcaaaaaaattataagacatccttaggaatatgctcggtgtgtaaccatctttatcaggttttcgtcaaacatattttgcttcagtcttctctcgtagttttttctatgcgatgcccctccttttcttgtgtctaaaggaaggggatttttttgtggaaaatctactttgaatttaaggag .........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 ctccttaaattcaaagtagattttccacaaaaaaatccccttcctttagacacaagaaaaggaggggcatcgcatagaaaaaactacgagagaagactgaagcaaaatatgtttgacgaaaacctgataaagatggttacacaccgagcatattcctaaggatgtcttataatttttttgatttaggaattaagaaagattatatatatcaagttttgatgtacttcacgcttgcatatccaagcggccttccccgtagttctgagcaactaatttgttctaggaaacatcttagttgctttttattttaaaacaactatattacggaacatcacagtctggattaacaaaagaatacaagatagtgactgattgtaaaaaaacattctttttttgctttctaaaaagcgactactgctaatccggggttggagtaaaaaatctctgccccttaagggaacagagatgaaat Mask Tandem Repeat Region ================================================ atttcatctctgttcccttaaggggcagagattttttactccaaccccggattagcagtagtcgctttttagaaagcaaaaaaagaatgtttttttacaatcagtcactatcttgtattcttttgttaatccagactgtgatgttccgtaatatagttgttttaaaataaaaagcaactaagatgtttcctagaacaaattagttgctcagaactacggggaaggccgcttggatatgcaagcgtgaagtacatcaaaacttgatatatataatctttcttaattcctaaatcaaaaaaattataagacatccttaggaatatgctcggtgtgtaaccatctttatcaggttttcgtcaaacatattttgcttcagtcttctctcgtagttttttctatgcgatgcccctccttttcttgtgtctaaaggaaggggatttttttgtggaaaatctactttgaatttaaggag Find is-nt database================================================ Query_seq: SSA_0227:SSA_0228|SSA_0227:SSA_0228:Collagen-binding surface protein, putative:hypothetical protein:->->:223031..223502 472 atttcatctctgttcccttaaggggcagagattttttactccaaccccggattagcagtagtcgctttttagaaagcaaaaaaagaatgtttttttacaatcagtcactatcttgtattcttttgttaatccagactgtgatgttccgtaatatagttgttttaaaataaaaagcaactaagatgtttcctagaacaaattagttgctcagaactacggggaaggccgcttggatatgcaagcgtgaagtacatcaaaacttgatatatataatctttcttaattcctaaatcaaaaaaattataagacatccttaggaatatgctcggtgtgtaaccatctttatcaggttttcgtcaaacatattttgcttcagtcttctctcgtagttttttctatgcgatgcccctccttttcttgtgtctaaaggaaggggatttttttgtggaaaatctactttgaatttaaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0227:SSA_0228|SSA_0227:SSA_0228:Collagen-binding surface protein, putative:hypothetical protein:->->:223031..223502 472 atttcatctctgttcccttaaggggcagagattttttactccaaccccggattagcagtagtcgctttttagaaagcaaaaaaagaatgtttttttacaatcagtcactatcttgtattcttttgttaatccagactgtgatgttccgtaatatagttgttttaaaataaaaagcaactaagatgtttcctagaacaaattagttgctcagaactacggggaaggccgcttggatatgcaagcgtgaagtacatcaaaacttgatatatataatctttcttaattcctaaatcaaaaaaattataagacatccttaggaatatgctcggtgtgtaaccatctttatcaggttttcgtcaaacatattttgcttcagtcttctctcgtagttttttctatgcgatgcccctccttttcttgtgtctaaaggaaggggatttttttgtggaaaatctactttgaatttaaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0227:SSA_0228|SSA_0227:SSA_0228:Collagen-binding surface protein, putative:hypothetical protein:->->:223031..223502 472 atttcatctctgttcccttaaggggcagagattttttactccaaccccggattagcagtagtcgctttttagaaagcaaaaaaagaatgtttttttacaatcagtcactatcttgtattcttttgttaatccagactgtgatgttccgtaatatagttgttttaaaataaaaagcaactaagatgtttcctagaacaaattagttgctcagaactacggggaaggccgcttggatatgcaagcgtgaagtacatcaaaacttgatatatataatctttcttaattcctaaatcaaaaaaattataagacatccttaggaatatgctcggtgtgtaaccatctttatcaggttttcgtcaaacatattttgcttcagtcttctctcgtagttttttctatgcgatgcccctccttttcttgtgtctaaaggaaggggatttttttgtggaaaatctactttgaatttaaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttcatctctgttcccttaaggggcagagattttttactccaaccccggattagcagtagtcgctttttagaaagcaaaaaaagaatgtttttttacaatcagtcactatcttgtattcttttgttaatccagactgtgatgttccgtaatatagttgttttaaaataaaaagcaactaagatgtttcctagaacaaattagttgctcagaactacggggaaggccgcttggatatgcaagcgtgaagtacatcaaaacttgatatatataatctttcttaattcctaaatcaaaaaaattataagacatccttaggaatatgctcggtgtgtaaccatctttatcaggttttcgtcaaacatattttgcttcagtcttctctcgtagttttttctatgcgatgcccctccttttcttgtgtctaaaggaaggggatttttttgtggaaaatctactttgaatttaaggag Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 6 End: 167 ..... M S V P L R G R D F L L Q P R I S S S R F L E S K K R M F F Y N Q S L S C I L L L I Q T V M F R N I V V L K ................................................................................................................................................................................................................................................................................................................. Protein_Len: 35 Strand: + Start: 320 End: 424 ............................................................................................................................................................................................................................................................................................................................... M C S V C N H L Y Q V F V K H I L L Q S S L V V F S M R C P S F S C V ................................................ Protein_Len: 53 Strand: - Start: 165 End: 323 .................................................................................................................................................................... F L F C S L H K R S C I L Q E S S R P L G S P Y A L T F Y M L V Q Y I Y D K K I G L D F F N Y S M R L F M ..................................................................................................................................................... Protein_Len: 41 Strand: - Start: 55 End: 177 ...................................................... C Y D S K L F C F F F T K K C D T V I K Y E K T L G S Q S T G Y Y L Q K L I F L M ....................................................................................................................................................................................................................................................................................................... atttcatctctgttcccttaaggggcagagattttttactccaaccccggattagcagtagtcgctttttagaaagcaaaaaaagaatgtttttttacaatcagtcactatcttgtattcttttgttaatccagactgtgatgttccgtaatatagttgttttaaaataaaaagcaactaagatgtttcctagaacaaattagttgctcagaactacggggaaggccgcttggatatgcaagcgtgaagtacatcaaaacttgatatatataatctttcttaattcctaaatcaaaaaaattataagacatccttaggaatatgctcggtgtgtaaccatctttatcaggttttcgtcaaacatattttgcttcagtcttctctcgtagttttttctatgcgatgcccctccttttcttgtgtctaaaggaaggggatttttttgtggaaaatctactttgaatttaaggag 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================================================ atttcatctctgttcccttaaggggcagagattttttactccaaccccggattagcagtagtcgctttttagaaagcaaaaaaagaatgtttttttacaatcagtcactatcttgtattcttttgttaatccagactgtgatgttccgtaatatagttgttttaaaataaaaagcaactaagatgtttcctagaacaaattagttgctcagaactacggggaaggccgcttggatatgcaagcgtgaagtacatcaaaacttgatatatataatctttcttaattcctaaatcaaaaaaattataagacatccttaggaatatgctcggtgtgtaaccatctttatcaggttttcgtcaaacatattttgcttcagtcttctctcgtagttttttctatgcgatgcccctccttttcttgtgtctaaaggaaggggatttttttgtggaaaatctactttgaatttaaggag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 57 HP_score: -4.3 Tail_Score: -3.85698 Start: 76 End: 98 Full_Region: agatagtgactgatt gtaaaaaaa cattc tttttttgc tttctaaaaagcgac ...........................................................................gtaaaaaaacattctttttttgc...................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 84 HP_score: -5.4 Tail_Score: -5.45802 Start: 174 End: 207 Full_Region: tccccgtagttctga gcaactaatttgtt ctagga aacatcttagttgc tttttattttaaaac .............................................................................................................................................................................gcaactaatttgttctaggaaacatcttagttgc......................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0227:SSA_0228|SSA_0227:SSA_0228:Collagen-binding surface protein, putative:hypothetical protein:->->:223031..223502 472 atttcatctctgttcccttaaggggcagagattttttactccaaccccggattagcagtagtcgctttttagaaagcaaaaaaagaatgtttttttacaatcagtcactatcttgtattcttttgttaatccagactgtgatgttccgtaatatagttgttttaaaataaaaagcaactaagatgtttcctagaacaaattagttgctcagaactacggggaaggccgcttggatatgcaagcgtgaagtacatcaaaacttgatatatataatctttcttaattcctaaatcaaaaaaattataagacatccttaggaatatgctcggtgtgtaaccatctttatcaggttttcgtcaaacatattttgcttcagtcttctctcgtagttttttctatgcgatgcccctccttttcttgtgtctaaaggaaggggatttttttgtggaaaatctactttgaatttaaggag Intra-Species Hit: Count: 1 Min: 1 Max: 472 Len: 472 Subject: NC_009009_SSA_0227_SSA_0228|Collagen-binding surface protein, putative:hypothetical protein|POSITIVE:POSITIVE|[223031,223502]|472 HSP 1 e-value: 0.0 bit: 769.0 Len: 472 Query Start:1 Query End:472 Subject Strand: POSITIVE Subject Start: 1 Subject End: 472 atttcatctctgttcccttaaggggcagagattttttactccaaccccggattagcagtagtcgctttttagaaagcnnnnnnngaatgnnnnnnnacaatcagtcactatcttgtattcttttgttaatccagactgtgatgttccgtaatatagttgttttaaaataaaaagcaactaagatgtttcctagaacaaattagttgctcagaactacggggaaggccgcttggatatgcaagcgtgaagtacatcaaaacttgatatatataatctttcttaattcctaaatcnnnnnnnttataagacatccttaggaatatgctcggtgtgtaaccatctttatcaggttttcgtcaaacatattttgcttcagtcttctctcgtagttttttctatgcgatgcccctccttttcttgtgtctaaaggaaggggannnnnnngtggaaaatctactttgaatttaaggag atttcatctctgttcccttaaggggcagagattttttactccaaccccggattagcagtagtcgctttttagaaagcaaaaaaagaatgtttttttacaatcagtcactatcttgtattcttttgttaatccagactgtgatgttccgtaatatagttgttttaaaataaaaagcaactaagatgtttcctagaacaaattagttgctcagaactacggggaaggccgcttggatatgcaagcgtgaagtacatcaaaacttgatatatataatctttcttaattcctaaatcaaaaaaattataagacatccttaggaatatgctcggtgtgtaaccatctttatcaggttttcgtcaaacatattttgcttcagtcttctctcgtagttttttctatgcgatgcccctccttttcttgtgtctaaaggaaggggatttttttgtggaaaatctactttgaatttaaggag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCAUCUCUGUUCCCUUAAGGGGCAGAGAUUUUUUACUCCAACCCCGGAUUAGCAGUAGUCGCUUUUUAGAAAGCAAAAAAAGAAUGUUUUUUUACAAUCAGUCACUAUCUUGUAUUCUUUUGUUAAUCCAGACUGUGAUGUUCCGUAAUAUAGUUGUUUUAAAAUAAAAAGCAACUAAGAUGUUUCCUAGAACAAAUUAGUUGCUCAGAACUACGGGGAAGGCCGCUUGGAUAUGCAAGCGUGAAGUACAUCAAAACUUGAUAUAUAUAAUCUUUCUUAAUUCCUAAAUCAAAAAAAUUAUAAGACAUCCUUAGGAAUAUGCUCGGUGUGUAACCAUCUUUAUCAGGUUUUCGUCAAACAUAUUUUGCUUCAGUCUUCUCUCGUAGUUUUUUCUAUGCGAUGCCCCUCCUUUUCUUGUGUCUAAAGGAAGGGGAUUUUUUUGUGGAAAAUCUACUUUGAAUUUAAGGAG .....(((((((((((.....)))))))))))......((((......((((((((((.((..(((((....))))).......((.(((......))).)).................)).)))))))))).....(((((.((((((((....(((((............(((((((((..(((((....)))))..))))))))).(((((((((((((((((((((((......)))))).((((((....(((((((((((................((((((((.......................))))))))......(((.....))).....))))))))))).(.....)......)))))).)))))).)))))))))))......))))).((((((((((.(....)...))))).)))))......)))))))).))).))...........)))) (-130.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCUUAAAUUCAAAGUAGAUUUUCCACAAAAAAAUCCCCUUCCUUUAGACACAAGAAAAGGAGGGGCAUCGCAUAGAAAAAACUACGAGAGAAGACUGAAGCAAAAUAUGUUUGACGAAAACCUGAUAAAGAUGGUUACACACCGAGCAUAUUCCUAAGGAUGUCUUAUAAUUUUUUUGAUUUAGGAAUUAAGAAAGAUUAUAUAUAUCAAGUUUUGAUGUACUUCACGCUUGCAUAUCCAAGCGGCCUUCCCCGUAGUUCUGAGCAACUAAUUUGUUCUAGGAAACAUCUUAGUUGCUUUUUAUUUUAAAACAACUAUAUUACGGAACAUCACAGUCUGGAUUAACAAAAGAAUACAAGAUAGUGACUGAUUGUAAAAAAACAUUCUUUUUUUGCUUUCUAAAAAGCGACUACUGCUAAUCCGGGGUUGGAGUAAAAAAUCUCUGCCCCUUAAGGGAACAGAGAUGAAAU ((((...........((.(((.((((...........((((((((((..........))))))))))......((((....(((((((.(.((((...(((((..((((((((((.....((((..........))))......))))))))))......(((((..((((((((((((((((....)))).)))))))))))).)))))..)))))...........((((((......))))))..)))).))))))))..((((((((((..((((......))))..))))))))))...............)))).....)))).)))))..(((((((((..((((((((.....(((((.....)))))........)))))))).(((((((....))))))).......)))))))))...))))......(((((((.(((....)))..)))))))..... (-120.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 430 384 122 76 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 325 350 307 51 2 NC_009009:SSA_1572|5end_hypothetical_protein_1575908..1576138_NEGATIVE 315 229 195 230 197 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 304 409 364 105 53 NC_009009:SSA_0129|5end_Translation_initiation_factor_IF-1,_putative_119957..120187_POSITIVE 303 57 15 64 24 NC_009009:SSA_0374|5end_Peptide_methionine_sulfoxide_reductase_msrA/msrB,_putative_363163..363393_POSITIVE 303 240 191 68 19 NC_009009:SSA_0173|5end_23S_rRNA_m1G745_methyltransferase,_putative_170535..170765_NEGATIVE 300 436 392 119 72 NC_009009:SSA_0159|5end_hypothetical_protein_155000..155230_POSITIVE 298 370 324 199 161 NC_009009:SSA_0870|5end_Cell_division_protein_FtsE,_putative_862936..863166_POSITIVE 297 410 370 75 28 NC_009009:SSA_2369|5end_hypothetical_protein_2371093..2371323_NEGATIVE 297 437 400 214 184 NC_009009:SSA_2044|5end_Cysteinyl-tRNA_synthetase,_putative_2048409..2048639_NEGATIVE 297 417 384 60 24 NC_009009:SSA_0405|5end_Transcriptional_regulator,_XRE_family,_putative_401418..401648_POSITIVE 296 419 374 103 65 NC_009009:SSA_2176|5end_hypothetical_protein_2175159..2175389_NEGATIVE 295 440 395 133 79 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 295 59 15 80 21 NC_009009:SSA_0395|5end_6-phospho-beta-glucosidase,_putative_391061..391291_POSITIVE 294 386 345 99 57 NC_009009:SSA_1747|5end_hypothetical_protein_1733450..1733680_NEGATIVE 293 423 381 112 56 NC_009009:SSA_1186|5end_Acetyltransferase,_CysE/LacA/Lpx_A/NodL_family,_putative_1215219..1215449_NEGATIVE 292 440 396 211 165 NC_009009:SSA_1839|5end_Cysteine_synthase,_putative_1832976..1833206_POSITIVE 291 431 397 125 85 NC_009009:SSA_0883|5end_Glycerate_kinase,_putative_877560..877790_POSITIVE 288 419 371 106 46 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 288 147 103 68 20 NC_009009:SSA_0443|5end_Possible_ABC-type_efflux_pump_permease_component,_putative_442877..443107_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 430 384 125 79 NC_009009:SSA_1049|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064971..1065121_POSITIVE 321 32 6 85 59 NC_009009:SSA_0227|3end_Collagen-binding_surface_protein,_putative_222970..223120_POSITIVE 316 437 395 46 10 NC_009009:SSA_0081|3end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_84220..84370_NEGATIVE 300 436 392 113 66 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 296 250 205 54 3 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 295 440 395 143 89 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 293 423 381 136 80 NC_009009:SSA_1187|3end_Transcriptional_antiterminator,_BglG_family,_putative_1215195..1215345_NEGATIVE 292 440 396 110 64 NC_009009:SSA_1837|3end_hypothetical_protein_1832955..1833105_POSITIVE 291 431 397 115 75 NC_009009:SSA_0882|3end_Phosphoserine_phosphatase,_putative_877630..877780_POSITIVE 290 65 21 131 75 NC_009009:SSA_1225|3end_Branched-chain_amino_acid_aminotransferase,_putative_1247589..1247739_NEGATIVE 289 410 364 110 61 NC_009009:SSA_1594|3end_Metalloendopeptidase,_putative_1598457..1598607_NEGATIVE 288 419 371 90 30 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 288 147 103 141 93 NC_009009:SSA_0442|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_443030..443180_POSITIVE 288 250 207 102 41 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 283 49 1 78 26 NC_009009:SSA_1612|3end_Diacylglycerol_kinase,_putative_1616099..1616249_NEGATIVE 283 420 371 80 35 NC_009009:SSA_0949|3end_hypothetical_protein_956395..956545_POSITIVE 281 434 395 120 72 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 280 388 342 121 74 NC_009009:SSA_1841|3end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1834422..1834572_NEGATIVE 278 419 375 67 13 NC_009009:SSA_0934|3end_HydD,_putative_944091..944241_POSITIVE 277 245 202 140 103 NC_009009:SSA_0638|3end_Tryptophan_synthase_alpha_chain,_putative_627794..627944_POSITIVE