Origin IGS: tttctcctatttgcaatataaaagtgttgatgtctaatccttattattttatagtaatttacccctaaaagcaaggttctttgaattattttcacaattctaatttttagattattcgaattaattcaaaaaatagtttgaagcatttattttttactcatgttttataaatctcatttttgttcacaaaaaagaactcctaaaaagagttctcgtttctaatt .........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 aattagaaacgagaactctttttaggagttcttttttgtgaacaaaaatgagatttataaaacatgagtaaaaaataaatgcttcaaactattttttgaattaattcgaataatctaaaaattagaattgtgaaaataattcaaagaaccttgcttttaggggtaaattactataaaataataaggattagacatcaacacttttatattgcaaataggagaaa Mask Tandem Repeat Region ================================================ tttctcctatttgcaatataaaagtgttgatgtctaatccttattattttatagtaatttacccctaaaagcaaggttctttgaattattttcacaattctaatttttagattattcgaattaattcaaaaaatagtttgaagcatttattttttactcatgttttataaatctcatttttgttcacaaaaaagaactcctaaaaagagttctcgtttctaatt Find is-nt database================================================ Query_seq: SSA_1541:SSA_1542|SSA_1541:SSA_1542:Peptidase, U32 family, putative:Peptidase, U32 family, putative:<-<-:1546691..1546914 224 tttctcctatttgcaatataaaagtgttgatgtctaatccttattattttatagtaatttacccctaaaagcaaggttctttgaattattttcacaattctaatttttagattattcgaattaattcaaaaaatagtttgaagcatttattttttactcatgttttataaatctcatttttgttcacaaaaaagaactcctaaaaagagttctcgtttctaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1541:SSA_1542|SSA_1541:SSA_1542:Peptidase, U32 family, putative:Peptidase, U32 family, putative:<-<-:1546691..1546914 224 tttctcctatttgcaatataaaagtgttgatgtctaatccttattattttatagtaatttacccctaaaagcaaggttctttgaattattttcacaattctaatttttagattattcgaattaattcaaaaaatagtttgaagcatttattttttactcatgttttataaatctcatttttgttcacaaaaaagaactcctaaaaagagttctcgtttctaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1541:SSA_1542|SSA_1541:SSA_1542:Peptidase, U32 family, putative:Peptidase, U32 family, putative:<-<-:1546691..1546914 224 tttctcctatttgcaatataaaagtgttgatgtctaatccttattattttatagtaatttacccctaaaagcaaggttctttgaattattttcacaattctaatttttagattattcgaattaattcaaaaaatagtttgaagcatttattttttactcatgttttataaatctcatttttgttcacaaaaaagaactcctaaaaagagttctcgtttctaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctcctatttgcaatataaaagtgttgatgtctaatccttattattttatagtaatttacccctaaaagcaaggttctttgaattattttcacaattctaatttttagattattcgaattaattcaaaaaatagtttgaagcatttattttttactcatgttttataaatctcatttttgttcacaaaaaagaactcctaaaaagagttctcgtttctaatt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 3 End: 125 .. R R N A I Y F H Q H R I R I I K Y Y N V G L L L T R Q I I K V I R I K L N N S N M ................................................................................................... tttctcctatttgcaatataaaagtgttgatgtctaatccttattattttatagtaatttacccctaaaagcaaggttctttgaattattttcacaattctaatttttagattattcgaattaattcaaaaaatagtttgaagcatttattttttactcatgttttataaatctcatttttgttcacaaaaaagaactcctaaaaagagttctcgtttctaatt 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: 84 Start: 26 End: 55 .........................GTTGATGTCTAATCCTTATTATTTTATAGT......................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 46 End: 75 .............................................CTTGCTTTTAGGGGTAAATTACTATAAAAT..................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttctcctatttgcaatataaaagtgttgatgtctaatccttattattttatagtaatttacccctaaaagcaaggttctttgaattattttcacaattctaatttttagattattcgaattaattcaaaaaatagtttgaagcatttattttttactcatgttttataaatctcatttttgttcacaaaaaagaactcctaaaaagagttctcgtttctaatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 42 HP_score: -2.8 Tail_Score: -3.36289 Start: 125 End: 142 Full_Region: gtaaaaaataaatgc ttcaaa ctattt tttgaa ttaattcgaataatc ............................................................................................................................ttcaaactattttttgaa.................................................................................. Find igs database================================================ Query_seq: SSA_1541:SSA_1542|SSA_1541:SSA_1542:Peptidase, U32 family, putative:Peptidase, U32 family, putative:<-<-:1546691..1546914 224 tttctcctatttgcaatataaaagtgttgatgtctaatccttattattttatagtaatttacccctaaaagcaaggttctttgaattattttcacaattctaatttttagattattcgaattaattcaaaaaatagtttgaagcatttattttttactcatgttttataaatctcatttttgttcacaaaaaagaactcctaaaaagagttctcgtttctaatt Intra-Species Hit: Count: 1 Min: 1 Max: 224 Len: 224 Subject: NC_009009_SSA_1541_SSA_1542|Peptidase, U32 family, putative:Peptidase, U32 family, putative|NEGATIVE:NEGATIVE|[1546691,1546914]|224 HSP 1 e-value: 1.0E-124 bit: 444.0 Len: 224 Query Start:1 Query End:224 Subject Strand: POSITIVE Subject Start: 1 Subject End: 224 tttctcctatttgcaatataaaagtgttgatgtctaatccttattattttatagtaatttacccctaaaagcaaggttctttgaattattttcacaattctaatttttagattattcgaattaattcaaaaaatagtttgaagcatttattttttactcatgttttataaatctcatttttgttcacaaaaaagaactcctaaaaagagttctcgtttctaatt tttctcctatttgcaatataaaagtgttgatgtctaatccttattattttatagtaatttacccctaaaagcaaggttctttgaattattttcacaattctaatttttagattattcgaattaattcaaaaaatagtttgaagcatttattttttactcatgttttataaatctcatttttgttcacaaaaaagaactcctaaaaagagttctcgtttctaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCCUAUUUGCAAUAUAAAAGUGUUGAUGUCUAAUCCUUAUUAUUUUAUAGUAAUUUACCCCUAAAAGCAAGGUUCUUUGAAUUAUUUUCACAAUUCUAAUUUUUAGAUUAUUCGAAUUAAUUCAAAAAAUAGUUUGAAGCAUUUAUUUUUUACUCAUGUUUUAUAAAUCUCAUUUUUGUUCACAAAAAAGAACUCCUAAAAAGAGUUCUCGUUUCUAAUU .........((((....(((((((((..(((..(((..((((....(((((..(((...)))...)))))..))))...(((((((((.(((......((((.....))))......))).)))))))))...)))..((((((((.............))))))))...))).)))))))))...))))..(((((((.......)))))))........... (-30.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAGAAACGAGAACUCUUUUUAGGAGUUCUUUUUUGUGAACAAAAAUGAGAUUUAUAAAACAUGAGUAAAAAAUAAAUGCUUCAAACUAUUUUUUGAAUUAAUUCGAAUAAUCUAAAAAUUAGAAUUGUGAAAAUAAUUCAAAGAACCUUGCUUUUAGGGGUAAAUUACUAUAAAAUAAUAAGGAUUAGACAUCAACACUUUUAUAUUGCAAAUAGGAGAAA ..(((.(((.(((((((((.....))))))))).))).))).......(((..((((.......((((((.........))).))).....((((((((((((.((((.....((((.....))))....))))..))))))))))))(((((.(((((..((((...)))).)))))...)))))..))))..)))...(((((((.......)))))))... (-37.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 745 80 31 171 122 NC_009009:SSA_1541|5end_Peptidase,_U32_family,_putative_1546600..1546830_NEGATIVE 260 219 179 203 162 NC_009009:SSA_1626|5end_DNA_translocase_ftsK,_putative_1629377..1629607_NEGATIVE 255 214 171 138 96 NC_009009:SSA_1031|5end_DNA_topology_modulation_protein_FlaR,_putative_1048255..1048485_NEGATIVE 246 109 68 104 68 NC_009009:SSA_1286|5end_hypothetical_protein_1306244..1306474_NEGATIVE 244 63 24 127 77 NC_009009:SSA_1823|5end_hypothetical_protein_1812513..1812743_NEGATIVE 234 50 2 165 114 NC_009009:SSA_1411|5end_Glucose-1-phosphate_thymidylytransferase,_putative_1423960..1424190_NEGATIVE 227 78 34 166 126 NC_009009:SSA_2004|5end_Zinc_metalloprotease_zmpB_precursor,_putative_2004930..2005160_NEGATIVE 223 80 32 194 146 NC_009009:SSA_1520|5end_Elongation_factor_Tu,_putative_1527581..1527811_NEGATIVE 213 80 35 119 68 NC_009009:SSA_2379|5end_Signal_transduction_protein_with_a_C-terminal_ATPase/histidine_kinase_domain,_putative_2385233..2385463_NEGATIVE 210 41 1 97 50 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 209 45 2 144 96 NC_009009:SSA_1299|5end_Maltose/maltodextrin_ABC_transport_system,_putative_1316629..1316859_POSITIVE 208 47 1 91 48 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 205 173 134 161 117 NC_009009:SSA_1513|5end_Glycosyltransferase,_putative_1520976..1521206_NEGATIVE 205 220 178 128 82 NC_009009:SSA_0393|5end_Bacteriocin_ABC-type_exporter,_ATP_binding/permease_protein,_putative_388766..388996_POSITIVE 203 78 31 201 153 NC_009009:SSA_1996|5end_DNA-directed_RNA_polymerase_delta_subunit,_putative_1994024..1994254_NEGATIVE 202 96 53 178 127 NC_009009:SSA_0049|5end_Dihydroxyacetone_kinase_(Dak1),_putative_53612..53842_POSITIVE 201 214 177 57 2 NC_009009:SSA_1599|5end_hypothetical_protein_1606416..1606646_NEGATIVE 200 42 1 137 91 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 197 35 1 134 93 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 194 108 71 202 168 NC_009009:SSA_1711|5end_Endonuclease_III,_putative_1699636..1699866_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 219 179 72 31 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 255 214 171 80 38 NC_009009:SSA_1032|3end_30S_ribosomal_protein_subunit_S20,_putative_1048313..1048463_NEGATIVE 246 109 68 93 57 NC_009009:SSA_1287|3end_hypothetical_protein_1306255..1306405_NEGATIVE 244 63 24 124 74 NC_009009:SSA_1824|3end_hypothetical_protein_1812516..1812666_NEGATIVE 234 50 2 131 80 NC_009009:SSA_1412|3end_hypothetical_protein_1423994..1424144_NEGATIVE 224 159 127 96 61 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 213 80 35 91 40 NC_009009:SSA_2394|3end_Competence_stimulating_peptide_2385261..2385411_NEGATIVE 210 41 1 100 53 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 209 45 2 62 14 NC_009009:SSA_1298|3end_Maltose/maltodextrin_ABC_transporter,_sugar-binding_protein_MalX,_putative_1316627..1316777_POSITIVE 205 173 134 136 92 NC_009009:SSA_1514|3end_Cell-wall_biogenesis_glycosyltransferase,_putative_1521001..1521151_NEGATIVE 203 78 31 63 15 NC_009009:SSA_1997|3end_Membrane_spanning_protein,_putative_1994162..1994312_NEGATIVE 201 80 46 54 9 NC_009009:SSA_2298|3end_Serine_protease_containing_a_PDZ_domain,_putative_2299569..2299719_NEGATIVE 200 186 142 45 2 NC_009009:SSA_1596|3end_hypothetical_protein_1602075..1602225_NEGATIVE 200 42 1 146 100 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 199 220 193 29 1 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 197 35 1 58 17 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 197 220 171 66 16 NC_009009:SSA_0750|3end_hypothetical_protein_732255..732405_POSITIVE 195 166 125 109 67 NC_009009:SSA_2169|3end_Glucose-1-phosphate_uridylyltransferase,_putative_2169485..2169635_POSITIVE 194 119 76 50 4 NC_009009:SSA_1717|3end_Modification_methylase_DpnIIB,_putative_1704155..1704305_NEGATIVE 194 108 71 107 73 NC_009009:SSA_1712|3end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1699731..1699881_NEGATIVE