Origin IGS: ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatttatataacaaaaatcctttgaaatcaacatttcaaaggattttttctttttgtttcaagccctaactgaacaacaaactcaatactagatctcgaaaaaaa .........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 tttttttcgagatctagtattgagtttgttgttcagttagggcttgaaacaaaaagaaaaaatcctttgaaatgttgatttcaaaggatttttgttatataaattatttaacttctgtaagagttaaataatttctattttagctgttagaaacgttggtacatcaatgtttctagaatgctacctaataaaaggtagagtgaatggtagagtag Mask Tandem Repeat Region ================================================ ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatttatataacaaaaatcctttgaaatcaacatttcaaaggattttttctttttgtttcaagccctaactgaacaacaaactcaatactagatctcgaaaaaaa Find is-nt database================================================ Query_seq: SSA_2295:SSA_2296|SSA_2295:SSA_2296:Integrase/recombinase, phage integrase family, putative:Transcriptional regulator, XRE family, putative:-><-:2298424..2298638 215 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatttatataacaaaaatcctttgaaatcaacatttcaaaggattttttctttttgtttcaagccctaactgaacaacaaactcaatactagatctcgaaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2295:SSA_2296|SSA_2295:SSA_2296:Integrase/recombinase, phage integrase family, putative:Transcriptional regulator, XRE family, putative:-><-:2298424..2298638 215 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatttatataacaaaaatcctttgaaatcaacatttcaaaggattttttctttttgtttcaagccctaactgaacaacaaactcaatactagatctcgaaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2295:SSA_2296|SSA_2295:SSA_2296:Integrase/recombinase, phage integrase family, putative:Transcriptional regulator, XRE family, putative:-><-:2298424..2298638 215 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatttatataacaaaaatcctttgaaatcaacatttcaaaggattttttctttttgtttcaagccctaactgaacaacaaactcaatactagatctcgaaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatttatataacaaaaatcctttgaaatcaacatttcaaaggattttttctttttgtttcaagccctaactgaacaacaaactcaatactagatctcgaaaaaaa Predict ORF larger than 30AA ================================================ ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatttatataacaaaaatcctttgaaatcaacatttcaaaggattttttctttttgtttcaagccctaactgaacaacaaactcaatactagatctcgaaaaaaa 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================================================ ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatttatataacaaaaatcctttgaaatcaacatttcaaaggattttttctttttgtttcaagccctaactgaacaacaaactcaatactagatctcgaaaaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 78 HP_score: -7.6 Tail_Score: -4.28254 Start: 79 End: 118 Full_Region: aaaggatttttgtta tataaattatttaacttct gta agagttaaataatttcta ttttagctgttagaa ..............................................................................tataaattatttaacttctgtaagagttaaataatttcta................................................................................................. TransTerm Strand: + Conf: 70 HP_score: -6.6 Tail_Score: -4.03234 Start: 85 End: 112 Full_Region: CAGCTAAAATAGAAA TTATTTAACTCT TAC AGAAGTTAAATAA TTTATATAACAAAAA ....................................................................................TTATTTAACTCTTACAGAAGTTAAATAA....................................................................................................... TransTerm Strand: - Conf: 76 HP_score: -6.6 Tail_Score: -4.46775 Start: 85 End: 112 Full_Region: tttttgttatataaa ttatttaacttct gta agagttaaataa tttctattttagctg ....................................................................................ttatttaacttctgtaagagttaaataa....................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -12.1 Tail_Score: -6.01725 Start: 128 End: 153 Full_Region: TTTATATAACAAAAA TCCTTTGAAAT CAAC ATTTCAAAGGA TTTTTTCTTTTTGTT ...............................................................................................................................TCCTTTGAAATCAACATTTCAAAGGA.............................................................. TransTerm Strand: - Conf: 100 HP_score: -12.1 Tail_Score: -5.24796 Start: 128 End: 153 Full_Region: aacaaaaagaaaaaa tcctttgaaat gttg atttcaaagga tttttgttatataaa ...............................................................................................................................tcctttgaaatgttgatttcaaagga.............................................................. Find igs database================================================ Query_seq: SSA_2295:SSA_2296|SSA_2295:SSA_2296:Integrase/recombinase, phage integrase family, putative:Transcriptional regulator, XRE family, putative:-><-:2298424..2298638 215 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatttatataacaaaaatcctttgaaatcaacatttcaaaggattttttctttttgtttcaagccctaactgaacaacaaactcaatactagatctcgaaaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 208 Len: 208 Subject: NC_009009_SSA_2295_SSA_2296|Integrase/recombinase, phage integrase family, putative:Transcriptional regulator, XRE family, putative|POSITIVE:NEGATIVE|[2298424,2298638]|215 HSP 1 e-value: 6.0E-93 bit: 341.0 Len: 208 Query Start:1 Query End:208 Subject Strand: POSITIVE Subject Start: 1 Subject End: 208 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatttatataacaaaaatcctttgaaatcaacatttcaaaggannnnnnnnnnnngtttcaagccctaactgaacaacaaactcaatactagatctcg....... ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatttatataacaaaaatcctttgaaatcaacatttcaaaggattttttctttttgtttcaagccctaactgaacaacaaactcaatactagatctcg....... Inter-species Hit: Count: 12 Min: 1 Max: 147 Len: 147 Subject: NC_004368_gbs2073_gbs2074|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2146033,2146462]|430 HSP 1 e-value: 2.0E-52 bit: 206.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataa....................................................................................................... ctactctaccattcactctaccttttattatgtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttactgaagttaaataa....................................................................................................... Subject: NC_007432_SAK_2059_SAK_2060|site-specific recombinase, phage integrase family:peptidase propeptide and YPEB domain protein|POSITIVE:POSITIVE|[2052058,2052556]|499 HSP 1 e-value: 9.0E-52 bit: 204.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatttatataacaaaaatcctttgaaatcaacatttc.................................................................... ctactctaccattcactctaccttttattatgtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactctcactgaagttaaataattga-atataaaaaagcctatgaaatcaatatttc.................................................................... Subject: NC_008023_MGAS2096_Spy1853_MGAS2096_Spy1854|hypothetical protein:Transcriptional regulator|POSITIVE:NEGATIVE|[1812375,1812753]|379 HSP 1 e-value: 5.0E-13 bit: 75.8 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 59 Subject End: 172 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatt..................................................................................................... ctactctaccattcactctaccttttattaagcaactatcaataaatattgatacaataaggtttataacagctaaaatagaaaatacttaacctttacagaagtaaaataatt..................................................................................................... Subject: NC_008021_MGAS9429_Spy1832_MGAS9429_Spy1833|hypothetical protein:transcriptional regulator|POSITIVE:NEGATIVE|[1788498,1788876]|379 HSP 1 e-value: 5.0E-13 bit: 75.8 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 59 Subject End: 172 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatt..................................................................................................... ctactctaccattcactctaccttttattaagcaactatcaataaatattgatacaataaggtttataacagctaaaatagaaaatacttaacctttacagaagtaaaataatt..................................................................................................... Subject: NC_007297_M5005_Spy_1821_M5005_Spy_1822|hypothetical protein:transcriptional regulator|POSITIVE:NEGATIVE|[1789166,1789640]|475 HSP 1 e-value: 5.0E-13 bit: 75.8 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 154 Subject End: 267 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatt..................................................................................................... ctactctaccattcactctaccttttattaagcaactatcaataaatattgatacaataaggtttataacagctaaaatagaaaatacttaacctttacagaagtaaaataatt..................................................................................................... Subject: NC_007296_M28_Spy1830_M28_Spy1831|hypothetical protein:transcriptional regulator|POSITIVE:NEGATIVE|[1837710,1838184]|475 HSP 1 e-value: 5.0E-13 bit: 75.8 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 154 Subject End: 267 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatt..................................................................................................... ctactctaccattcactctaccttttattaagcaactatcaataaatattgatacaataaggtttataacagctaaaatagaaaatacttaacctttacagaagtaaaataatt..................................................................................................... Subject: NC_006086_M6_Spy1840_M6_Spy1841|hypothetical protein:Transcriptional regulator|POSITIVE:NEGATIVE|[1849995,1850469]|475 HSP 1 e-value: 5.0E-13 bit: 75.8 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 154 Subject End: 267 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatt..................................................................................................... ctactctaccattcactctaccttttattaagcaactatcaataaatattgatacaataaggtttataacagctaaaatagaaaatacttaacctttacagaagtaaaataatt..................................................................................................... Subject: NC_004606_SPs1820_SPs1821|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1846094,1846568]|475 HSP 1 e-value: 5.0E-13 bit: 75.8 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 154 Subject End: 267 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatt..................................................................................................... ctactctaccattcactctaccttttattaagcaactatcaataaatattgatacaataaggtttataacagctaaaatagaaaatacttaacctttacagaagtaaaataatt..................................................................................................... Subject: NC_004070_SpyM3_1822_SpyM3_1823|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1852309,1852783]|475 HSP 1 e-value: 5.0E-13 bit: 75.8 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 154 Subject End: 267 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatt..................................................................................................... ctactctaccattcactctaccttttattaagcaactatcaataaatattgatacaataaggtttataacagctaaaatagaaaatacttaacctttacagaagtaaaataatt..................................................................................................... Subject: NC_003485_spyM18_2203_spyM18_2207|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1847060,1848268]|1209 HSP 1 e-value: 5.0E-13 bit: 75.8 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 154 Subject End: 267 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatt..................................................................................................... ctactctaccattcactctaccttttattaagcaactatcaataaatattgatacaataaggtttataacagctaaaatagaaaatacttaacctttacagaagtaaaataatt..................................................................................................... Subject: NC_002737_SPy2166_SPy2169|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1803082,1804291]|1210 HSP 1 e-value: 5.0E-13 bit: 75.8 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 154 Subject End: 267 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatt..................................................................................................... ctactctaccattcactctaccttttattaagcaactatcaataaatattgatacaataaggtttataacagctaaaatagaaaatacttaacctttacagaagtaaaataatt..................................................................................................... Subject: NC_008024_MGAS10750_Spy1938_MGAS10750_Spy1939|hypothetical protein:Transcriptional regulator|POSITIVE:NEGATIVE|[1892822,1893296]|475 HSP 1 e-value: 1.0E-10 bit: 67.9 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 154 Subject End: 267 ctactctaccattcactctaccttttattaggtagcattctagaaacattgatgtaccaacgtttctaacagctaaaatagaaattatttaactcttacagaagttaaataatt..................................................................................................... ctactctaccattcactctaccttttattaagcaactatcaataaatattgatacaataaggtttataacagctaaaatagaaaatacttaacctttacagaagcaaaataatt..................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUACUCUACCAUUCACUCUACCUUUUAUUAGGUAGCAUUCUAGAAACAUUGAUGUACCAACGUUUCUAACAGCUAAAAUAGAAAUUAUUUAACUCUUACAGAAGUUAAAUAAUUUAUAUAACAAAAAUCCUUUGAAAUCAACAUUUC ...........((((..((((((......)))))).....(((((((.(((......))).))))))).........(((.((((((((((((((.....).))))))))))))).))).............))))........... (-26.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAUGUUGAUUUCAAAGGAUUUUUGUUAUAUAAAUUAUUUAACUUCUGUAAGAGUUAAAUAAUUUCUAUUUUAGCUGUUAGAAACGUUGGUACAUCAAUGUUUCUAGAAUGCUACCUAAUAAAAGGUAGAGUGAAUGGUAGAGUAG (((((....)))))..................((((((((((((((......))))))))))))))((((((((.(..(((((((((((((....)))))))))))))....((((((......)))))).......).)))))))) (-38.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 57 15 69 27 NC_009009:SSA_1394|5end_hypothetical_protein_1409048..1409278_NEGATIVE 258 41 11 110 71 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 236 66 22 159 120 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 233 52 11 129 93 NC_009009:SSA_1515|5end_hypothetical_protein_1522129..1522359_NEGATIVE 218 60 15 195 141 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 218 60 15 61 7 NC_009009:SSA_1552|5end_hypothetical_protein_1554913..1555143_POSITIVE 218 67 21 50 6 NC_009009:SSA_0283|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIB_component,_putative_274559..274789_POSITIVE 217 140 93 153 100 NC_009009:SSA_0852|5end_ATP-dependent_DNA_helicase,_putative_839050..839280_POSITIVE 215 80 36 77 22 NC_009009:SSA_0318|5end_Secreted_metalloendopeptidase_Gcp_311701..311931_POSITIVE 213 43 9 119 88 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 207 60 11 54 10 NC_009009:SSA_0660|5end_Cell_division_protein_DivIVA,_putative_643798..644028_POSITIVE 206 59 13 135 88 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 206 49 1 91 47 NC_009009:SSA_0016|5end_ComX1,_transcriptional_regulator_of_competence-specific_genes,_putative_15487..15717_POSITIVE 204 35 1 113 78 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 203 43 5 161 118 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 202 73 35 58 15 NC_009009:SSA_2145|5end_Tributyrin_esterase,_putative_2146658..2146888_NEGATIVE 200 58 12 157 106 NC_009009:SSA_1981|5end_hypothetical_protein_1975421..1975651_NEGATIVE 198 67 21 126 79 NC_009009:SSA_2118|5end_Thiamine_pyrophosphokinase,_putative_2120500..2120730_NEGATIVE 198 41 5 130 95 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 198 75 31 132 92 NC_009009:SSA_1691|5end_Transcriptional_regulator,_XRE_family,_putative_1683281..1683511_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 57 15 72 30 NC_009009:SSA_1395|3end_hypothetical_protein_1409045..1409195_NEGATIVE 233 52 11 129 93 NC_009009:SSA_1516|3end_Cell-wall_biogenesis_glycosyltransferase,_putative_1522129..1522279_NEGATIVE 215 80 36 87 32 NC_009009:SSA_0317|3end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311791..311941_POSITIVE 213 43 9 109 78 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 213 58 12 86 39 NC_009009:SSA_0459|3end_hypothetical_protein_462513..462663_POSITIVE 212 140 111 121 88 NC_009009:SSA_1169|3end_Conserved_hypothetical_protein_with_an_alpha/beta_hydrolase_fold,_putative_1196846..1196996_POSITIVE 204 35 1 54 19 NC_009009:SSA_0538|3end_PduH_protein,_putative_534254..534404_POSITIVE 200 58 12 151 100 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 198 41 5 107 72 NC_009009:SSA_1879|3end_Glycyl-tRNA_synthetase_beta_chain,_putative_1872223..1872373_NEGATIVE 198 75 31 119 79 NC_009009:SSA_1690|3end_hypothetical_protein_1683348..1683498_POSITIVE 197 73 31 118 69 NC_009009:SSA_2334|3end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2336457..2336607_NEGATIVE 196 59 13 134 69 NC_009009:SSA_1929|3end_Macrophage_infectivity_potentiator_protein,_putative_1917029..1917179_NEGATIVE 194 60 12 44 1 NC_009009:SSA_0659|3end_hypothetical_protein_643868..644018_POSITIVE 194 40 5 38 6 NC_009009:SSA_0509|3end_Propanediol_utilization_protein,_putative_508538..508688_POSITIVE 193 39 4 147 97 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 193 75 39 45 4 NC_009009:SSA_1299|3end_Maltose/maltodextrin_ABC_transport_system,_putative_1318067..1318217_POSITIVE 192 73 31 107 65 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 191 75 33 58 16 NC_009009:SSA_2295|3end_Integrase/recombinase,_phage_integrase_family,_putative_2298363..2298513_POSITIVE 191 41 1 91 47 NC_009009:SSA_2092|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095697..2095847_NEGATIVE 190 64 27 130 90 NC_009009:SSA_0814|3end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_795519..795669_NEGATIVE