Origin IGS: gccattccttgcagaaactcagactagtgaaaaaacattgctagtaagcgatatatctcatgacagctatttgattttcgactatataaaggataccagatgatgcttcattcactcttcactcaaaaaaataggccaaacattttttggcttgttttttcgccctcattcttctactgattggaggactctatctctacctgcgctttggcattcccagctactcccatcggcaactgatagaaacgctgagccatcctttcaagaaaagtccagcccagaacatcatcatagatctgcgcttacctagaggaattgcagctctgctagtcggagctagcttggccgtttcaggagccatc .........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 gatggctcctgaaacggccaagctagctccgactagcagagctgcaattcctctaggtaagcgcagatctatgatgatgttctgggctggacttttcttgaaaggatggctcagcgtttctatcagttgccgatgggagtagctgggaatgccaaagcgcaggtagagatagagtcctccaatcagtagaagaatgagggcgaaaaaacaagccaaaaaatgtttggcctatttttttgagtgaagagtgaatgaagcatcatctggtatcctttatatagtcgaaaatcaaatagctgtcatgagatatatcgcttactagcaatgttttttcactagtctgagtttctgcaaggaatggc Mask Tandem Repeat Region ================================================ gccattccttgcagaaactcagactagtgaaaaaacattgctagtaagcgatatatctcatgacagctatttgattttcgactatataaaggataccagatgatgcttcattcactcttcactcaaaaaaataggccaaacattttttggcttgttttttcgccctcattcttctactgattggaggactctatctctacctgcgctttggcattcccagctactcccatcggcaactgatagaaacgctgagccatcctttcaagaaaagtccagcccagaacatcatcatagatctgcgcttacctagaggaattgcagctctgctagtcggagctagcttggccgtttcaggagccatc Find is-nt database================================================ Query_seq: SSA_1742:SSA_1743|SSA_1742:SSA_1743:Ferrichrome-binding protein, putative:ABC-type Fe3+-siderophore transport system, permease component, putative:->->:1729948..1730309 362 gccattccttgcagaaactcagactagtgaaaaaacattgctagtaagcgatatatctcatgacagctatttgattttcgactatataaaggataccagatgatgcttcattcactcttcactcaaaaaaataggccaaacattttttggcttgttttttcgccctcattcttctactgattggaggactctatctctacctgcgctttggcattcccagctactcccatcggcaactgatagaaacgctgagccatcctttcaagaaaagtccagcccagaacatcatcatagatctgcgcttacctagaggaattgcagctctgctagtcggagctagcttggccgtttcaggagccatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1742:SSA_1743|SSA_1742:SSA_1743:Ferrichrome-binding protein, putative:ABC-type Fe3+-siderophore transport system, permease component, putative:->->:1729948..1730309 362 gccattccttgcagaaactcagactagtgaaaaaacattgctagtaagcgatatatctcatgacagctatttgattttcgactatataaaggataccagatgatgcttcattcactcttcactcaaaaaaataggccaaacattttttggcttgttttttcgccctcattcttctactgattggaggactctatctctacctgcgctttggcattcccagctactcccatcggcaactgatagaaacgctgagccatcctttcaagaaaagtccagcccagaacatcatcatagatctgcgcttacctagaggaattgcagctctgctagtcggagctagcttggccgtttcaggagccatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1742:SSA_1743|SSA_1742:SSA_1743:Ferrichrome-binding protein, putative:ABC-type Fe3+-siderophore transport system, permease component, putative:->->:1729948..1730309 362 gccattccttgcagaaactcagactagtgaaaaaacattgctagtaagcgatatatctcatgacagctatttgattttcgactatataaaggataccagatgatgcttcattcactcttcactcaaaaaaataggccaaacattttttggcttgttttttcgccctcattcttctactgattggaggactctatctctacctgcgctttggcattcccagctactcccatcggcaactgatagaaacgctgagccatcctttcaagaaaagtccagcccagaacatcatcatagatctgcgcttacctagaggaattgcagctctgctagtcggagctagcttggccgtttcaggagccatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 204 Max: 311 Len: 108 Subject: UniRef90_Q2ZYB0 Cluster: Transport system permease protein precursor; n=1; Streptococcus suis 89/1591|Rep: Transport system permease protein precursor - Streptococcus suis 89/1591 HSP 1 e-value: 1.0E-6 bit: 54.7 Len: 108 Query Start:204 Query End:311 Subject Strand: null Subject Start: 37 Subject End: 72 ........................................................................................................................................................................................................... R F G I P S Y S H R Q L I E T L S H P F K K S P A Q N I I I D L R L P R ................................................... ........................................................................................................................................................................................................... R F G A I S Y S H Q Q L M E T L T H P L T D S S A Q D V I I D L R L P R ................................................... gccattccttgcagaaactcagactagtgaaaaaacattgctagtaagcgatatatctcatgacagctatttgattttcgactatataaaggataccagatgatgcttcattcactcttcactcaaaaaaataggccaaacattttttggcttgttttttcgccctcattcttctactgattggaggactctatctctacctgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggaattgcagctctgctagtcggagctagcttggccgtttcaggagccatc Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 110 End: 307 ............................................................................................................. M H S S L K K I G Q T F F G L F F R P H S S T D W R T L S L P A L W H S Q L L P S A T D R N A E P S F Q E K S S P E H H ....................................................... Protein_Len: 60 Strand: + Start: 147 End: 362 .................................................................................................................................................. M A C F F A L I L L L I G G L Y L Y L R F G I P S Y S H R Q L I E T L S H P F K K S P A Q N I I I D L R L P R G I A A L Protein_Len: 46 Strand: - Start: 224 End: 361 ............................................................................................................................................................................................................................... E W R C S I S V S L W G K L F L G A W F M M M S R R K G L P I A A R S T P A L K A T E P A M . Protein_Len: 40 Strand: - Start: 177 End: 296 ................................................................................................................................................................................ Q N S S E I E V Q A K A N G A V G M P L Q Y F R Q A M R E L F T W G L V D D Y M .................................................................. gccattccttgcagaaactcagactagtgaaaaaacattgctagtaagcgatatatctcatgacagctatttgattttcgactatataaaggataccagatgatgcttcattcactcttcactcaaaaaaataggccaaacattttttggcttgttttttcgccctcattcttctactgattggaggactctatctctacctgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggaattgcagctctgctagtcggagctagcttggccgtttcaggagccatc 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================================================ gccattccttgcagaaactcagactagtgaaaaaacattgctagtaagcgatatatctcatgacagctatttgattttcgactatataaaggataccagatgatgcttcattcactcttcactcaaaaaaataggccaaacattttttggcttgttttttcgccctcattcttctactgattggaggactctatctctacctgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggaattgcagctctgctagtcggagctagcttggccgtttcaggagccatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 77 HP_score: -4.9 Tail_Score: -5.03715 Start: 132 End: 154 Full_Region: CTTCACTCAAAAAAA TAGGCCAAA CATTT TTTGGCTTG TTTTTTCGCCCTCAT ...................................................................................................................................TAGGCCAAACATTTTTTGGCTTG................................................................................................................................................................................................................ TransTerm Strand: - Conf: 61 HP_score: -3.1 Tail_Score: -4.37763 Start: 134 End: 152 Full_Region: gagggcgaaaaaaca agccaaa aaatg tttggcc tatttttttgagtga .....................................................................................................................................agccaaaaaatgtttggcc.................................................................................................................................................................................................................. TransTerm Strand: + Conf: 79 HP_score: -6.6 Tail_Score: -4.62085 Start: 135 End: 151 Full_Region: CACTCAAAAAAATAG GCCAAA CATTT TTTGGC TTGTTTTTTCGCCCT ......................................................................................................................................GCCAAACATTTTTTGGC................................................................................................................................................................................................................... TransTerm Strand: - Conf: 59 HP_score: -6.6 Tail_Score: -3.21573 Start: 135 End: 151 Full_Region: agggcgaaaaaacaa gccaaa aaatg tttggc ctatttttttgagtg ......................................................................................................................................gccaaaaaatgtttggc................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1742:SSA_1743|SSA_1742:SSA_1743:Ferrichrome-binding protein, putative:ABC-type Fe3+-siderophore transport system, permease component, putative:->->:1729948..1730309 362 gccattccttgcagaaactcagactagtgaaaaaacattgctagtaagcgatatatctcatgacagctatttgattttcgactatataaaggataccagatgatgcttcattcactcttcactcaaaaaaataggccaaacattttttggcttgttttttcgccctcattcttctactgattggaggactctatctctacctgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggaattgcagctctgctagtcggagctagcttggccgtttcaggagccatc Intra-Species Hit: Count: 1 Min: 1 Max: 362 Len: 362 Subject: NC_009009_SSA_1742_SSA_1743|Ferrichrome-binding protein, putative:ABC-type Fe3+-siderophore transport system, permease component, putative|POSITIVE:POSITIVE|[1729948,1730309]|362 HSP 1 e-value: 4.0E-98 bit: 359.0 Len: 202 Query Start:1 Query End:202 Subject Strand: POSITIVE Subject Start: 1 Subject End: 202 gccattccttgcagaaactcagactagtgaaaaaacattgctagtaagcgatatatctcatgacagctatttgattttcgactatataaaggataccagatgatgcttcattcactcttcactcnnnnnnntaggccaaacattttttggcttgttttttcgccctcattcttctactgattggaggactctatctctacct................................................................................................................................................................ gccattccttgcagaaactcagactagtgaaaaaacattgctagtaagcgatatatctcatgacagctatttgattttcgactatataaaggataccagatgatgcttcattcactcttcactcaaaaaaataggccaaacattttttggcttgttttttcgccctcattcttctactgattggaggactctatctctacct................................................................................................................................................................ HSP 2 e-value: 3.0E-19 bit: 97.6 Len: 49 Query Start:314 Query End:362 Subject Strand: POSITIVE Subject Start: 314 Subject End: 362 .........................................................................................................................................................................................................................................................................................................................aattgcagctctgctagtcggagctagcttggccgtttcaggagccatc .........................................................................................................................................................................................................................................................................................................................aattgcagctctgctagtcggagctagcttggccgtttcaggagccatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCAUUCCUUGCAGAAACUCAGACUAGUGAAAAAACAUUGCUAGUAAGCGAUAUAUCUCAUGACAGCUAUUUGAUUUUCGACUAUAUAAAGGAUACCAGAUGAUGCUUCAUUCACUCUUCACUCAAAAAAAUAGGCCAAACAUUUUUUGGCUUGUUUUUUCGCCCUCAUUCUUCUACUGAUUGGAGGACUCUAUCUCUACCUGCGCUUUGGCAUUCCCAGCUACUCCCAUCGGCAACUGAUAGAAACGCUGAGCCAUCCUUUCAAGAAAAGUCCAGCCCAGAACAUCAUCAUAGAUCUGCGCUUACCUAGAGGAAUUGCAGCUCUGCUAGUCGGAGCUAGCUUGGCCGUUUCAGGAGCCAUC ((((.....(((((.......((..(((((......((((((....)))))).......((((.(((((((((...(((...........)))...))))))..))))))))))))..)).....(((((((((((((((.....)))))))))))))))...((((..((.......))...)))).............)))))...))))...........((((.((((....).))).(((((((..(((..((((((.......((...(((.((((...((......)))))).)))...)))))))).....(((((((.....))))))).)))..).)))))).))))..... (-92.31) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGGCUCCUGAAACGGCCAAGCUAGCUCCGACUAGCAGAGCUGCAAUUCCUCUAGGUAAGCGCAGAUCUAUGAUGAUGUUCUGGGCUGGACUUUUCUUGAAAGGAUGGCUCAGCGUUUCUAUCAGUUGCCGAUGGGAGUAGCUGGGAAUGCCAAAGCGCAGGUAGAGAUAGAGUCCUCCAAUCAGUAGAAGAAUGAGGGCGAAAAAACAAGCCAAAAAAUGUUUGGCCUAUUUUUUUGAGUGAAGAGUGAAUGAAGCAUCAUCUGGUAUCCUUUAUAUAGUCGAAAAUCAAAUAGCUGUCAUGAGAUAUAUCGCUUACUAGCAAUGUUUUUUCACUAGUCUGAGUUUCUGCAAGGAAUGGC ..(((((........))))).((((..(((.....((((((((......((((......(((.((((((......))...)))).)))...(((((.((((..(((.(((((...((((((((((((((((.....).)))))))....(((......))).)))))))).))))).)))..)))).)))))...)))).((((((((...((((((.....))))))...))))))))...((..((((((.(((((((...((((((..(..(((((..(((.....((......))...))).)))))..)..))))))..)))))))))))))..))..)).))))))..))).)))) (-100.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 423 359 319 207 156 NC_009009:SSA_0410|5end_hypothetical_protein_406442..406672_NEGATIVE 403 359 318 46 1 NC_009009:SSA_1369|5end_FmtA-like_protein,_putative_1385929..1386159_NEGATIVE 402 359 318 174 119 NC_009009:SSA_0179|5end_hypothetical_protein_183966..184196_POSITIVE 401 349 306 70 22 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 400 260 211 158 93 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 398 359 311 174 119 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 392 227 188 77 43 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 387 359 311 118 71 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 386 354 311 64 8 NC_009009:SSA_0272|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_266023..266253_POSITIVE 372 360 318 181 122 NC_009009:SSA_1560|5end_Structural_maintenance_of_chromosome_protein_(chromosome_segregation_ATPase),_putative_1565194..1565424_NEGATIVE 372 350 301 183 128 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 370 360 311 205 151 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 369 338 291 227 173 NC_009009:SSA_1721|5end_DNA_polymerase_III,_delta'_subunit,_putative_1708028..1708258_NEGATIVE 367 359 312 222 165 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 362 360 313 195 133 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 360 359 318 46 1 NC_009009:SSA_1368|5end_hypothetical_protein_1384077..1384307_NEGATIVE 358 357 323 218 180 NC_009009:SSA_0697|5end_hypothetical_protein_680083..680313_POSITIVE 358 358 319 144 103 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 354 360 322 150 103 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 353 360 318 182 141 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 349 306 77 29 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 388 353 316 61 10 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 387 359 311 118 71 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 382 350 303 133 87 NC_009009:SSA_0895|3end_ATP-binding_cassette_transporter-like_protein,_putative_887763..887913_POSITIVE 381 249 201 53 6 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 370 360 311 147 93 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 364 354 319 54 3 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 361 360 311 148 106 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 360 255 211 148 108 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 358 358 319 147 106 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 354 350 310 151 109 NC_009009:SSA_0411|3end_hypothetical_protein_406480..406630_NEGATIVE 354 360 322 133 86 NC_009009:SSA_0278|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_272382..272532_POSITIVE 353 360 318 64 23 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 352 348 301 113 71 NC_009009:SSA_1368|3end_hypothetical_protein_1383748..1383898_NEGATIVE 350 300 253 69 12 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 346 209 163 114 64 NC_009009:SSA_1238|3end_hypothetical_protein_1262402..1262552_NEGATIVE 345 220 171 76 30 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 344 341 302 72 30 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 344 299 251 54 2 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 342 360 316 148 91 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE