Origin IGS: gtataagataagagtaaaatgtttaagttattttaaggaagttttaagaaatggatattatactataaccaagttaagaaattaacttaactcctaaaacttttttctttttaaaaaataatctccctacaaaaagccaccaaacggtggttttttgctattttcagacatgagaggggcagggcttgccagttttcaacgagaatcaggaaactgtaaacgattcagggctagtttttgccattattttgttataatagatagcgaggtattct .........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 agaatacctcgctatctattataacaaaataatggcaaaaactagccctgaatcgtttacagtttcctgattctcgttgaaaactggcaagccctgcccctctcatgtctgaaaatagcaaaaaaccaccgtttggtggctttttgtagggagattattttttaaaaagaaaaaagttttaggagttaagttaatttcttaacttggttatagtataatatccatttcttaaaacttccttaaaataacttaaacattttactcttatcttatac Mask Tandem Repeat Region ================================================ gtataagataagagtaaaatgtttaagttattttaaggaagttttaagaaatggatattatactataaccaagttaagaaattaacttaactcctaaaacttttttctttttaaaaaataatctccctacaaaaagccaccaaacggtggttttttgctattttcagacatgagaggggcagggcttgccagttttcaacgagaatcaggaaactgtaaacgattcagggctagtttttgccattattttgttataatagatagcgaggtattct Find is-nt database================================================ Query_seq: SSA_0064:SSA_0065|SSA_0064:SSA_0065:hypothetical protein:Low molecular weight phosphotyrosine protein phosphatase, putative:->->:67040..67314 275 gtataagataagagtaaaatgtttaagttattttaaggaagttttaagaaatggatattatactataaccaagttaagaaattaacttaactcctaaaacttttttctttttaaaaaataatctccctacaaaaagccaccaaacggtggttttttgctattttcagacatgagaggggcagggcttgccagttttcaacgagaatcaggaaactgtaaacgattcagggctagtttttgccattattttgttataatagatagcgaggtattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0064:SSA_0065|SSA_0064:SSA_0065:hypothetical protein:Low molecular weight phosphotyrosine protein phosphatase, putative:->->:67040..67314 275 gtataagataagagtaaaatgtttaagttattttaaggaagttttaagaaatggatattatactataaccaagttaagaaattaacttaactcctaaaacttttttctttttaaaaaataatctccctacaaaaagccaccaaacggtggttttttgctattttcagacatgagaggggcagggcttgccagttttcaacgagaatcaggaaactgtaaacgattcagggctagtttttgccattattttgttataatagatagcgaggtattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0064:SSA_0065|SSA_0064:SSA_0065:hypothetical protein:Low molecular weight phosphotyrosine protein phosphatase, putative:->->:67040..67314 275 gtataagataagagtaaaatgtttaagttattttaaggaagttttaagaaatggatattatactataaccaagttaagaaattaacttaactcctaaaacttttttctttttaaaaaataatctccctacaaaaagccaccaaacggtggttttttgctattttcagacatgagaggggcagggcttgccagttttcaacgagaatcaggaaactgtaaacgattcagggctagtttttgccattattttgttataatagatagcgaggtattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtataagataagagtaaaatgtttaagttattttaaggaagttttaagaaatggatattatactataaccaagttaagaaattaacttaactcctaaaacttttttctttttaaaaaataatctccctacaaaaagccaccaaacggtggttttttgctattttcagacatgagaggggcagggcttgccagttttcaacgagaatcaggaaactgtaaacgattcagggctagtttttgccattattttgttataatagatagcgaggtattct Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 81 End: 170 ................................................................................ M N L T P K T F F F L K N N L P T K S H Q T V V F C Y F Q T ......................................................................................................... Protein_Len: 33 Strand: + Start: 118 End: 216 ..................................................................................................................... M I S L Q K A T K R W F F A I F R H E R G R A C Q F S T R I R K L ........................................................... Protein_Len: 40 Strand: + Start: 155 End: 274 .......................................................................................................................................................... M L F S D M R G A G L A S F Q R E S G N C K R F R A S F C H Y F V I I D S E V F . Protein_Len: 37 Strand: - Start: 114 End: 224 ................................................................................................................. F I I E R C F A V L R H N K A I K L C S L P L A Q W N E V L I L F S Y V M ................................................... gtataagataagagtaaaatgtttaagttattttaaggaagttttaagaaatggatattatactataaccaagttaagaaattaacttaactcctaaaacttttttctttttaaaaaataatctccctacaaaaagccaccaaacggtggttttttgctattttcagacatgagaggggcagggcttgccagttttcaacgagaatcaggaaactgtaaacgattcagggctagtttttgccattattttgttataatagatagcgaggtattct 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: 83 Start: 57 End: 86 ........................................................GTTAATTTCTTAACTTGGTTATAGTATAAT............................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtataagataagagtaaaatgtttaagttattttaaggaagttttaagaaatggatattatactataaccaagttaagaaattaacttaactcctaaaacttttttctttttaaaaaataatctccctacaaaaagccaccaaacggtggttttttgctattttcagacatgagaggggcagggcttgccagttttcaacgagaatcaggaaactgtaaacgattcagggctagtttttgccattattttgttataatagatagcgaggtattct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -9.4 Tail_Score: -4.09685 Start: 128 End: 160 Full_Region: AAAAAATAATCTCCC TACAAAAAGCCACC AAAC GGTGGTTTTTTGCTA TTTTCAGACATGAGA ...............................................................................................................................TACAAAAAGCCACCAAACGGTGGTTTTTTGCTA................................................................................................................... TransTerm Strand: + Conf: 86 HP_score: -10.1 Tail_Score: -3.64716 Start: 129 End: 158 Full_Region: AAAAATAATCTCCCT ACAAAAAGCCACC AAAC GGTGGTTTTTTGC TATTTTCAGACATGA ................................................................................................................................ACAAAAAGCCACCAAACGGTGGTTTTTTGC..................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -13.6 Tail_Score: -2.78508 Start: 130 End: 157 Full_Region: AAAATAATCTCCCTA CAAAAAGCCACC AAAC GGTGGTTTTTTG CTATTTTCAGACATG .................................................................................................................................CAAAAAGCCACCAAACGGTGGTTTTTTG...................................................................................................................... TransTerm Strand: - Conf: 70 HP_score: -4.6 Tail_Score: -4.83169 Start: 136 End: 151 Full_Region: tgaaaatagcaaaaa accacc gttt ggtggc tttttgtagggagat .......................................................................................................................................accaccgtttggtggc............................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -8.1 Tail_Score: -5.36314 Start: 137 End: 150 Full_Region: TCTCCCTACAAAAAG CCACC AAAC GGTGG TTTTTTGCTATTTTC ........................................................................................................................................CCACCAAACGGTGG............................................................................................................................. TransTerm Strand: - Conf: 73 HP_score: -8.1 Tail_Score: -3.49419 Start: 137 End: 150 Full_Region: gaaaatagcaaaaaa ccacc gttt ggtgg ctttttgtagggaga ........................................................................................................................................ccaccgtttggtgg............................................................................................................................. Find igs database================================================ Query_seq: SSA_0064:SSA_0065|SSA_0064:SSA_0065:hypothetical protein:Low molecular weight phosphotyrosine protein phosphatase, putative:->->:67040..67314 275 gtataagataagagtaaaatgtttaagttattttaaggaagttttaagaaatggatattatactataaccaagttaagaaattaacttaactcctaaaacttttttctttttaaaaaataatctccctacaaaaagccaccaaacggtggttttttgctattttcagacatgagaggggcagggcttgccagttttcaacgagaatcaggaaactgtaaacgattcagggctagtttttgccattattttgttataatagatagcgaggtattct Intra-Species Hit: Count: 1 Min: 1 Max: 275 Len: 275 Subject: NC_009009_SSA_0064_SSA_0065|hypothetical protein:Low molecular weight phosphotyrosine protein phosphatase, putative|POSITIVE:POSITIVE|[67040,67314]|275 HSP 1 e-value: 1.0E-133 bit: 474.0 Len: 275 Query Start:1 Query End:275 Subject Strand: POSITIVE Subject Start: 1 Subject End: 275 gtataagataagagtaaaatgtttaagttattttaaggaagttttaagaaatggatattatactataaccaagttaagaaattaacttaactcctaaaacnnnnnnnnnnnnaaaaaataatctccctacaaaaagccaccaaacggtggttttttgctattttcagacatgagaggggcagggcttgccagttttcaacgagaatcaggaaactgtaaacgattcagggctagtttttgccattattttgttataatagatagcgaggtattct gtataagataagagtaaaatgtttaagttattttaaggaagttttaagaaatggatattatactataaccaagttaagaaattaacttaactcctaaaacttttttctttttaaaaaataatctccctacaaaaagccaccaaacggtggttttttgctattttcagacatgagaggggcagggcttgccagttttcaacgagaatcaggaaactgtaaacgattcagggctagtttttgccattattttgttataatagatagcgaggtattct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUAAGAUAAGAGUAAAAUGUUUAAGUUAUUUUAAGGAAGUUUUAAGAAAUGGAUAUUAUACUAUAACCAAGUUAAGAAAUUAACUUAACUCCUAAAACUUUUUUCUUUUUAAAAAAUAAUCUCCCUACAAAAAGCCACCAAACGGUGGUUUUUUGCUAUUUUCAGACAUGAGAGGGGCAGGGCUUGCCAGUUUUCAACGAGAAUCAGGAAACUGUAAACGAUUCAGGGCUAGUUUUUGCCAUUAUUUUGUUAUAAUAGAUAGCGAGGUAUUCU ...........(((.......((((((.......((((((((((((.((..(((.(((......))).))).(((((....))))).....)).))))))))))))...)))))).......)))....((((((((((((....))))))))))))...((((((....)))))).(((((((((.(((.((((((...))))))(((....)))............))).)).)))))))..(((((((((((.....))))))))))).... (-66.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUACCUCGCUAUCUAUUAUAACAAAAUAAUGGCAAAAACUAGCCCUGAAUCGUUUACAGUUUCCUGAUUCUCGUUGAAAACUGGCAAGCCCUGCCCCUCUCAUGUCUGAAAAUAGCAAAAAACCACCGUUUGGUGGCUUUUUGUAGGGAGAUUAUUUUUUAAAAAGAAAAAAGUUUUAGGAGUUAAGUUAAUUUCUUAACUUGGUUAUAGUAUAAUAUCCAUUUCUUAAAACUUCCUUAAAAUAACUUAAACAUUUUACUCUUAUCUUAUAC (((.......(((((.((((.......)))))))))..................(((((.((((......((((..(((((((..((((.....)))).(((((.....(....)..(((((((.(((((....))))).))))))).))))).....)))))))..))))..(((((((((((((((((.......)))))).(((.(((......))).)))..))))))))))).........)))))))))............)))..... (-53.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 198 159 199 160 NC_009009:SSA_1626|5end_DNA_translocase_ftsK,_putative_1629377..1629607_NEGATIVE 331 206 161 167 115 NC_009009:SSA_1638|5end_hypothetical_protein_1641325..1641555_NEGATIVE 330 210 163 194 144 NC_009009:SSA_1892|5end_hypothetical_protein_1889262..1889492_NEGATIVE 328 218 171 65 8 NC_009009:SSA_1400|5end_Pyridoxal_kinase,_putative_1413072..1413302_NEGATIVE 328 219 171 56 9 NC_009009:SSA_1390|5end_hypothetical_protein_1406118..1406348_NEGATIVE 323 180 135 67 9 NC_009009:SSA_0728|5end_Protease,_putative_713688..713918_POSITIVE 315 197 152 131 83 NC_009009:SSA_0308|5end_hypothetical_protein_304385..304615_POSITIVE 312 218 177 224 178 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 307 190 143 53 5 NC_009009:SSA_1043|5end_Homoserine_dehydrogenase,_putative_1058565..1058795_POSITIVE 306 199 159 177 137 NC_009009:SSA_2109|5end_Elongation_factor_G,_putative_2114868..2115098_NEGATIVE 305 188 146 162 121 NC_009009:SSA_2333|5end_Integral_membrane_protein,_putative_2336460..2336690_NEGATIVE 305 210 165 102 44 NC_009009:SSA_2081|5end_hypothetical_protein_2085309..2085539_POSITIVE 304 185 145 177 138 NC_009009:SSA_1558|5end_Hydrolase,_HAD_superfamily_1560862..1561092_NEGATIVE 303 187 145 150 101 NC_009009:SSA_2047|5end_hypothetical_protein_2049953..2050183_NEGATIVE 302 198 151 204 148 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 301 206 167 73 38 NC_009009:SSA_0879|5end_Cell_division_regulator,_negative_regulator_of_FtsZ_septation_ring_formation,_putative_873632..873862_POSITIVE 299 189 142 185 134 NC_009009:SSA_0990|5end_hypothetical_protein_991733..991963_POSITIVE 299 209 164 168 112 NC_009009:SSA_0632|5end_Anthranilate_synthase_component_I,_putative_621458..621688_POSITIVE 297 211 171 84 42 NC_009009:SSA_1890|5end_Acetyltransferase,_putative_1888145..1888375_NEGATIVE 288 208 165 223 177 NC_009009:SSA_0317|5end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311259..311489_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 190 143 129 74 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE 333 173 131 107 58 NC_009009:SSA_1435|3end_hypothetical_protein_1441751..1441901_NEGATIVE 332 198 159 68 29 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 318 138 92 150 108 NC_009009:SSA_2162|3end_hypothetical_protein_2160815..2160965_POSITIVE 315 197 152 79 31 NC_009009:SSA_0307|3end_Glutamine_synthetase_type_1,_putative_304413..304563_POSITIVE 313 199 153 74 19 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 309 204 161 151 101 NC_009009:SSA_1639|3end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1641339..1641489_NEGATIVE 303 187 145 119 70 NC_009009:SSA_2048|3end_Serine_acetyltransferase,_putative_2049984..2050134_NEGATIVE 298 180 131 90 34 NC_009009:SSA_1453|3end_hypothetical_protein_1459897..1460047_NEGATIVE 297 211 171 83 41 NC_009009:SSA_1891|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888146..1888296_NEGATIVE 284 203 172 71 38 NC_009009:SSA_0208|3end_Conserved_uncharacterized_protein_204968..205118_NEGATIVE 284 190 151 73 25 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 283 188 167 144 123 NC_009009:SSA_2292|3end_DNA_segregation_ATPase_FtsK/SpoIIIE-like_protein,_putative_2295353..2295503_POSITIVE 282 198 151 83 41 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 281 190 148 49 2 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 281 210 162 53 4 NC_009009:SSA_1763|3end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750951..1751101_POSITIVE 279 190 145 79 34 NC_009009:SSA_2005|3end_Chaperone_protein_dnaJ,_putative_2005251..2005401_NEGATIVE 277 190 150 67 21 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 276 190 146 148 108 NC_009009:SSA_0492|3end_NADH-dependent_flavin_oxidoreductase,_putative_492771..492921_POSITIVE 275 190 146 83 38 NC_009009:SSA_1739|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1727065..1727215_POSITIVE