Origin IGS: aacagatatgattcccagtagaagtatgctggataaggaactgcagctggctgcaacttagtaagggggtgaaagcctatcgacacggaatttataaagggcctttacagccctcacgaggtagcagcggtctgacagaacccttaatctgttaatacgagaaagaaggaatttatgacaa .........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 ttgtcataaattccttctttctcgtattaacagattaagggttctgtcagaccgctgctacctcgtgagggctgtaaaggccctttataaattccgtgtcgataggctttcacccccttactaagttgcagccagctgcagttccttatccagcatacttctactgggaatcatatctgtt Mask Tandem Repeat Region ================================================ aacagatatgattcccagtagaagtatgctggataaggaactgcagctggctgcaacttagtaagggggtgaaagcctatcgacacggaatttataaagggcctttacagccctcacgaggtagcagcggtctgacagaacccttaatctgttaatacgagaaagaaggaatttatgacaa Find is-nt database================================================ Query_seq: SSA_1047:SSA_1048|SSA_1047:SSA_1048:UDP-N-acetylenolpyruvoylglucosamine reductase, putative:ABC transporter ATP-binding protein-spermidine/putrescine transport, putative:->->:1062906..1063086 181 aacagatatgattcccagtagaagtatgctggataaggaactgcagctggctgcaacttagtaagggggtgaaagcctatcgacacggaatttataaagggcctttacagccctcacgaggtagcagcggtctgacagaacccttaatctgttaatacgagaaagaaggaatttatgacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1047:SSA_1048|SSA_1047:SSA_1048:UDP-N-acetylenolpyruvoylglucosamine reductase, putative:ABC transporter ATP-binding protein-spermidine/putrescine transport, putative:->->:1062906..1063086 181 aacagatatgattcccagtagaagtatgctggataaggaactgcagctggctgcaacttagtaagggggtgaaagcctatcgacacggaatttataaagggcctttacagccctcacgaggtagcagcggtctgacagaacccttaatctgttaatacgagaaagaaggaatttatgacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1047:SSA_1048|SSA_1047:SSA_1048:UDP-N-acetylenolpyruvoylglucosamine reductase, putative:ABC transporter ATP-binding protein-spermidine/putrescine transport, putative:->->:1062906..1063086 181 aacagatatgattcccagtagaagtatgctggataaggaactgcagctggctgcaacttagtaagggggtgaaagcctatcgacacggaatttataaagggcctttacagccctcacgaggtagcagcggtctgacagaacccttaatctgttaatacgagaaagaaggaatttatgacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacagatatgattcccagtagaagtatgctggataaggaactgcagctggctgcaacttagtaagggggtgaaagcctatcgacacggaatttataaagggcctttacagccctcacgaggtagcagcggtctgacagaacccttaatctgttaatacgagaaagaaggaatttatgacaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 33 End: 152 ................................ M R N C S W L Q L S K G V K A Y R H G I Y K G P L Q P S R G S S G L T E P L I C ............................. Protein_Len: 32 Strand: - Start: 61 End: 156 ............................................................ Y P P S L R D V R F K Y L A K V A R V L Y C R D S L V R L R N M ......................... Protein_Len: 31 Strand: - Start: 3 End: 95 .. L Y S E W Y F Y A P Y P V A A P Q L K T L P H F G I S V S N M ...................................................................................... aacagatatgattcccagtagaagtatgctggataaggaactgcagctggctgcaacttagtaagggggtgaaagcctatcgacacggaatttataaagggcctttacagccctcacgaggtagcagcggtctgacagaacccttaatctgttaatacgagaaagaaggaatttatgacaa 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================================================ aacagatatgattcccagtagaagtatgctggataaggaactgcagctggctgcaacttagtaagggggtgaaagcctatcgacacggaatttataaagggcctttacagccctcacgaggtagcagcggtctgacagaacccttaatctgttaatacgagaaagaaggaatttatgacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1047:SSA_1048|SSA_1047:SSA_1048:UDP-N-acetylenolpyruvoylglucosamine reductase, putative:ABC transporter ATP-binding protein-spermidine/putrescine transport, putative:->->:1062906..1063086 181 aacagatatgattcccagtagaagtatgctggataaggaactgcagctggctgcaacttagtaagggggtgaaagcctatcgacacggaatttataaagggcctttacagccctcacgaggtagcagcggtctgacagaacccttaatctgttaatacgagaaagaaggaatttatgacaa Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_009009_SSA_1047_SSA_1048|UDP-N-acetylenolpyruvoylglucosamine reductase, putative:ABC transporter ATP-binding protein-spermidine/putrescine transport, putative|POSITIVE:POSITIVE|[1062906,1063086]|181 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 aacagatatgattcccagtagaagtatgctggataaggaactgcagctggctgcaacttagtaagggggtgaaagcctatcgacacggaatttataaagggcctttacagccctcacgaggtagcagcggtctgacagaacccttaatctgttaatacgagaaagaaggaatttatgacaa aacagatatgattcccagtagaagtatgctggataaggaactgcagctggctgcaacttagtaagggggtgaaagcctatcgacacggaatttataaagggcctttacagccctcacgaggtagcagcggtctgacagaacccttaatctgttaatacgagaaagaaggaatttatgacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGAUAUGAUUCCCAGUAGAAGUAUGCUGGAUAAGGAACUGCAGCUGGCUGCAACUUAGUAAGGGGGUGAAAGCCUAUCGACACGGAAUUUAUAAAGGGCCUUUACAGCCCUCACGAGGUAGCAGCGGUCUGACAGAACCCUUAAUCUGUUAAUACGAGAAAGAAGGAAUUUAUGACAA (((((((.......((((((......)))))).(((((..((((((.(.(((((.((((.((.((((.(((((.((((....................)))).)))))..)))).)).)))).))))).).))).)))...))))))))))))............................ (-55.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUCAUAAAUUCCUUCUUUCUCGUAUUAACAGAUUAAGGGUUCUGUCAGACCGCUGCUACCUCGUGAGGGCUGUAAAGGCCCUUUAUAAAUUCCGUGUCGAUAGGCUUUCACCCCCUUACUAAGUUGCAGCCAGCUGCAGUUCCUUAUCCAGCAUACUUCUACUGGGAAUCAUAUCUGUU ............................(((((((..((((..(((.(((...(((((.((...(((((((..((.((((((..(((((.......))).))..)))))).)).)))))))...)).)))))...))))))..)))).(((((..........)))))......))))))) (-50.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 70 27 229 186 NC_009009:SSA_1419|5end_hypothetical_protein_1429675..1429905_NEGATIVE 343 57 11 58 14 NC_009009:SSA_1274|5end_hypothetical_protein_1297454..1297684_NEGATIVE 343 150 110 188 147 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 335 130 81 230 164 NC_009009:SSA_1850|5end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1846024..1846254_NEGATIVE 330 50 15 231 198 NC_009009:SSA_1739|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1725540..1725770_POSITIVE 329 139 96 157 111 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 329 90 43 192 136 NC_009009:SSA_0018|5end_Cell-shape_determining_protein_MreD,_putative_23628..23858_POSITIVE 327 152 111 147 99 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 326 70 27 166 128 NC_009009:SSA_1264|5end_hypothetical_protein_1290042..1290272_NEGATIVE 322 79 37 216 172 NC_009009:SSA_0940|5end_NOL1/NOP2/sun_family_protein,_putative_947626..947856_POSITIVE 320 69 22 62 15 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 318 136 100 223 182 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 317 137 98 204 167 NC_009009:SSA_0423|5end_hypothetical_protein_421347..421577_NEGATIVE 316 139 101 88 34 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 314 59 11 184 129 NC_009009:SSA_1430|5end_Ribonuclease_Z,_putative_1438036..1438266_NEGATIVE 313 146 101 215 159 NC_009009:SSA_2072|5end_Phosphatidate_cytidylyltransferase,_putative_2075603..2075833_NEGATIVE 313 135 100 43 2 NC_009009:SSA_2020|5end_hypothetical_protein_2019284..2019514_POSITIVE 313 69 28 173 119 NC_009009:SSA_1647|5end_hypothetical_protein_1647169..1647399_NEGATIVE 311 149 101 67 14 NC_009009:SSA_1113|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_domain_and_a_winged-helix_DNA-binding_domains),_putative_1139742..1139972_POSITIVE 306 143 109 76 31 NC_009009:SSA_2107|5end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2111106..2111336_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 82 43 148 102 NC_009009:SSA_1498|3end_50S_ribosomal_protein_L20,_putative_1503753..1503903_NEGATIVE 327 152 111 147 99 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 320 69 22 65 18 NC_009009:SSA_1463|3end_Shikimate_kinase,_putative_1469764..1469914_NEGATIVE 316 139 101 77 23 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 314 142 101 113 74 NC_009009:SSA_2293|3end_hypothetical_protein_2295955..2296105_POSITIVE 310 144 102 147 97 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 305 84 41 74 30 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 300 78 31 73 16 NC_009009:SSA_1773|3end_hypothetical_protein_1759535..1759685_NEGATIVE 295 76 41 77 39 NC_009009:SSA_2197|3end_hypothetical_protein_2197314..2197464_NEGATIVE 295 85 41 139 100 NC_009009:SSA_0587|3end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_579761..579911_POSITIVE 294 69 28 83 55 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 293 53 15 77 29 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 292 49 13 80 44 NC_009009:SSA_1039|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1055389..1055539_POSITIVE 292 79 31 61 15 NC_009009:SSA_0261|3end_ABC-type_Mn2+/Zn2+_transport_systems,_permease_component,_putative_254605..254755_NEGATIVE 289 78 40 85 39 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 288 150 116 72 34 NC_009009:SSA_1780|3end_Tyrosine_recombinase_xerD,_putative_1766416..1766566_NEGATIVE 286 132 99 150 123 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 286 59 11 134 93 NC_009009:SSA_1978|3end_Dihydroxyacetone_kinase_family_protein_(Dak2_domain),_putative_1972269..1972419_NEGATIVE 284 71 41 150 115 NC_009009:SSA_1890|3end_Acetyltransferase,_putative_1887693..1887843_NEGATIVE 283 160 111 49 2 NC_009009:SSA_2000|3end_hypothetical_protein_1996987..1997137_NEGATIVE