Origin IGS: tttgctcctcctttgatttaatgaaccgtatgtacatctttcctttatttttccaaagccggaagaatactaagcactatcgctttttcaatgcctacagcaaccttttatcattttgttaactatattataaggcaaagaaatttttcctactagttgattttgtcaccggctgacatgacaaatgtcactattctgcttttagagcacaaagctagcaaatattggaataatctgtttatctcccttctgcatgaagacacaaaaaagccggtccccctcgttgagaggagccgactagttgtatgtctgttgcaatttagatagaaactggaattaaagtagcctaatctaaaaaatttttcaataaactagctactcaatttgtaagatgaggtgaccaacgctttttaaact .........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 agtttaaaaagcgttggtcacctcatcttacaaattgagtagctagtttattgaaaaattttttagattaggctactttaattccagtttctatctaaattgcaacagacatacaactagtcggctcctctcaacgagggggaccggcttttttgtgtcttcatgcagaagggagataaacagattattccaatatttgctagctttgtgctctaaaagcagaatagtgacatttgtcatgtcagccggtgacaaaatcaactagtaggaaaaatttctttgccttataatatagttaacaaaatgataaaaggttgctgtaggcattgaaaaagcgatagtgcttagtattcttccggctttggaaaaataaaggaaagatgtacatacggttcattaaatcaaaggaggagcaaa Mask Tandem Repeat Region ================================================ tttgctcctcctttgatttaatgaaccgtatgtacatctttcctttatttttccaaagccggaagaatactaagcactatcgctttttcaatgcctacagcaaccttttatcattttgttaactatattataaggcaaagaaatttttcctactagttgattttgtcaccggctgacatgacaaatgtcactattctgcttttagagcacaaagctagcaaatattggaataatctgtttatctcccttctgcatgaagacacaaaaaagccggtccccctcgttgagaggagccgactagttgtatgtctgttgcaatttagatagaaactggaattaaagtagcctaatctaaaaaatttttcaataaactagctactcaatttgtaagatgaggtgaccaacgctttttaaact Find is-nt database================================================ Query_seq: SSA_1975:SSA_1976|SSA_1975:SSA_1976:ABC-type multidrug transport system, ATPase component, putative:Conserved uncharacterized protein:<-<-:1971223..1971639 417 tttgctcctcctttgatttaatgaaccgtatgtacatctttcctttatttttccaaagccggaagaatactaagcactatcgctttttcaatgcctacagcaaccttttatcattttgttaactatattataaggcaaagaaatttttcctactagttgattttgtcaccggctgacatgacaaatgtcactattctgcttttagagcacaaagctagcaaatattggaataatctgtttatctcccttctgcatgaagacacaaaaaagccggtccccctcgttgagaggagccgactagttgtatgtctgttgcaatttagatagaaactggaattaaagtagcctaatctaaaaaatttttcaataaactagctactcaatttgtaagatgaggtgaccaacgctttttaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1975:SSA_1976|SSA_1975:SSA_1976:ABC-type multidrug transport system, ATPase component, putative:Conserved uncharacterized protein:<-<-:1971223..1971639 417 tttgctcctcctttgatttaatgaaccgtatgtacatctttcctttatttttccaaagccggaagaatactaagcactatcgctttttcaatgcctacagcaaccttttatcattttgttaactatattataaggcaaagaaatttttcctactagttgattttgtcaccggctgacatgacaaatgtcactattctgcttttagagcacaaagctagcaaatattggaataatctgtttatctcccttctgcatgaagacacaaaaaagccggtccccctcgttgagaggagccgactagttgtatgtctgttgcaatttagatagaaactggaattaaagtagcctaatctaaaaaatttttcaataaactagctactcaatttgtaagatgaggtgaccaacgctttttaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1975:SSA_1976|SSA_1975:SSA_1976:ABC-type multidrug transport system, ATPase component, putative:Conserved uncharacterized protein:<-<-:1971223..1971639 417 tttgctcctcctttgatttaatgaaccgtatgtacatctttcctttatttttccaaagccggaagaatactaagcactatcgctttttcaatgcctacagcaaccttttatcattttgttaactatattataaggcaaagaaatttttcctactagttgattttgtcaccggctgacatgacaaatgtcactattctgcttttagagcacaaagctagcaaatattggaataatctgtttatctcccttctgcatgaagacacaaaaaagccggtccccctcgttgagaggagccgactagttgtatgtctgttgcaatttagatagaaactggaattaaagtagcctaatctaaaaaatttttcaataaactagctactcaatttgtaagatgaggtgaccaacgctttttaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgctcctcctttgatttaatgaaccgtatgtacatctttcctttatttttccaaagccggaagaatactaagcactatcgctttttcaatgcctacagcaaccttttatcattttgttaactatattataaggcaaagaaatttttcctactagttgattttgtcaccggctgacatgacaaatgtcactattctgcttttagagcacaaagctagcaaatattggaataatctgtttatctcccttctgcatgaagacacaaaaaagccggtccccctcgttgagaggagccgactagttgtatgtctgttgcaatttagatagaaactggaattaaagtagcctaatctaaaaaatttttcaataaactagctactcaatttgtaagatgaggtgaccaacgctttttaaact Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 21 End: 119 .................... M N R M Y I F P L F F Q S R K N T K H Y R F F N A Y S N L L S F C .......................................................................................................................................................................................................................................................................................................... Protein_Len: 56 Strand: + Start: 157 End: 324 ............................................................................................................................................................ M I L S P A D M T N V T I L L L E H K A S K Y W N N L F I S L L H E D T K K P V P L V E R S R L V V C L L Q F R ............................................................................................. Protein_Len: 60 Strand: - Start: 156 End: 368 ........................................................................................................................................................... V I R S K S C L A L L Y Q F L R N I E R R C S S V F F G T G R T S L L R S T T H R N C N L Y F S S N F Y G L R F F K E M ................................................. tttgctcctcctttgatttaatgaaccgtatgtacatctttcctttatttttccaaagccggaagaatactaagcactatcgctttttcaatgcctacagcaaccttttatcattttgttaactatattataaggcaaagaaatttttcctactagttgattttgtcaccggctgacatgacaaatgtcactattctgcttttagagcacaaagctagcaaatattggaataatctgtttatctcccttctgcatgaagacacaaaaaagccggtccccctcgttgagaggagccgactagttgtatgtctgttgcaatttagatagaaactggaattaaagtagcctaatctaaaaaatttttcaataaactagctactcaatttgtaagatgaggtgaccaacgctttttaaact 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: 339 End: 368 ..................................................................................................................................................................................................................................................................................................................................................ATTGAAAAATTTTTTAGATTAGGCTACTTT................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 110 End: 139 .............................................................................................................TTTGCCTTATAATATAGTTAACAAAATGAT...................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgctcctcctttgatttaatgaaccgtatgtacatctttcctttatttttccaaagccggaagaatactaagcactatcgctttttcaatgcctacagcaaccttttatcattttgttaactatattataaggcaaagaaatttttcctactagttgattttgtcaccggctgacatgacaaatgtcactattctgcttttagagcacaaagctagcaaatattggaataatctgtttatctcccttctgcatgaagacacaaaaaagccggtccccctcgttgagaggagccgactagttgtatgtctgttgcaatttagatagaaactggaattaaagtagcctaatctaaaaaatttttcaataaactagctactcaatttgtaagatgaggtgaccaacgctttttaaact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -5.2 Tail_Score: -2.64331 Start: 174 End: 190 Full_Region: GATTTTGTCACCGGC TGACAT GACAA ATGTCA CTATTCTGCTTTTAG .............................................................................................................................................................................TGACATGACAAATGTCA................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -10.9 Tail_Score: -5.47431 Start: 270 End: 298 Full_Region: acagacatacaacta gtcggctcctctc aac gagggggaccggc ttttttgtgtcttca .............................................................................................................................................................................................................................................................................gtcggctcctctcaacgagggggaccggc....................................................................................................................... Find igs database================================================ Query_seq: SSA_1975:SSA_1976|SSA_1975:SSA_1976:ABC-type multidrug transport system, ATPase component, putative:Conserved uncharacterized protein:<-<-:1971223..1971639 417 tttgctcctcctttgatttaatgaaccgtatgtacatctttcctttatttttccaaagccggaagaatactaagcactatcgctttttcaatgcctacagcaaccttttatcattttgttaactatattataaggcaaagaaatttttcctactagttgattttgtcaccggctgacatgacaaatgtcactattctgcttttagagcacaaagctagcaaatattggaataatctgtttatctcccttctgcatgaagacacaaaaaagccggtccccctcgttgagaggagccgactagttgtatgtctgttgcaatttagatagaaactggaattaaagtagcctaatctaaaaaatttttcaataaactagctactcaatttgtaagatgaggtgaccaacgctttttaaact Intra-Species Hit: Count: 1 Min: 1 Max: 417 Len: 417 Subject: NC_009009_SSA_1975_SSA_1976|ABC-type multidrug transport system, ATPase component, putative:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[1971223,1971639]|417 HSP 1 e-value: 0.0 bit: 827.0 Len: 417 Query Start:1 Query End:417 Subject Strand: POSITIVE Subject Start: 1 Subject End: 417 tttgctcctcctttgatttaatgaaccgtatgtacatctttcctttatttttccaaagccggaagaatactaagcactatcgctttttcaatgcctacagcaaccttttatcattttgttaactatattataaggcaaagaaatttttcctactagttgattttgtcaccggctgacatgacaaatgtcactattctgcttttagagcacaaagctagcaaatattggaataatctgtttatctcccttctgcatgaagacacaaaaaagccggtccccctcgttgagaggagccgactagttgtatgtctgttgcaatttagatagaaactggaattaaagtagcctaatctaaaaaatttttcaataaactagctactcaatttgtaagatgaggtgaccaacgctttttaaact tttgctcctcctttgatttaatgaaccgtatgtacatctttcctttatttttccaaagccggaagaatactaagcactatcgctttttcaatgcctacagcaaccttttatcattttgttaactatattataaggcaaagaaatttttcctactagttgattttgtcaccggctgacatgacaaatgtcactattctgcttttagagcacaaagctagcaaatattggaataatctgtttatctcccttctgcatgaagacacaaaaaagccggtccccctcgttgagaggagccgactagttgtatgtctgttgcaatttagatagaaactggaattaaagtagcctaatctaaaaaatttttcaataaactagctactcaatttgtaagatgaggtgaccaacgctttttaaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGCUCCUCCUUUGAUUUAAUGAACCGUAUGUACAUCUUUCCUUUAUUUUUCCAAAGCCGGAAGAAUACUAAGCACUAUCGCUUUUUCAAUGCCUACAGCAACCUUUUAUCAUUUUGUUAACUAUAUUAUAAGGCAAAGAAAUUUUUCCUACUAGUUGAUUUUGUCACCGGCUGACAUGACAAAUGUCACUAUUCUGCUUUUAGAGCACAAAGCUAGCAAAUAUUGGAAUAAUCUGUUUAUCUCCCUUCUGCAUGAAGACACAAAAAAGCCGGUCCCCCUCGUUGAGAGGAGCCGACUAGUUGUAUGUCUGUUGCAAUUUAGAUAGAAACUGGAAUUAAAGUAGCCUAAUCUAAAAAAUUUUUCAAUAAACUAGCUACUCAAUUUGUAAGAUGAGGUGACCAACGCUUUUUAAACU ............(((((..(((((.....................(((((((((......)))))))))..((((......))))......(((.....)))........)))))..))))).....(((.(((((...((((((.............))))))((((((...((((((.....)))))).(((..(((.....(((.....((((((....((((((((....................((((...((((((((...((.(((..((.(((...))).))..))).))..))))..))))..)))).(((((((((..(((........)))...)).))))))).....))))))))..)))))).))).....)))..))).))))))....))))).)))... (-83.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUAAAAAGCGUUGGUCACCUCAUCUUACAAAUUGAGUAGCUAGUUUAUUGAAAAAUUUUUUAGAUUAGGCUACUUUAAUUCCAGUUUCUAUCUAAAUUGCAACAGACAUACAACUAGUCGGCUCCUCUCAACGAGGGGGACCGGCUUUUUUGUGUCUUCAUGCAGAAGGGAGAUAAACAGAUUAUUCCAAUAUUUGCUAGCUUUGUGCUCUAAAAGCAGAAUAGUGACAUUUGUCAUGUCAGCCGGUGACAAAAUCAACUAGUAGGAAAAAUUUCUUUGCCUUAUAAUAUAGUUAACAAAAUGAUAAAAGGUUGCUGUAGGCAUUGAAAAAGCGAUAGUGCUUAGUAUUCUUCCGGCUUUGGAAAAAUAAAGGAAAGAUGUACAUACGGUUCAUUAAAUCAAAGGAGGAGCAAA .............(((.((.(((((((((.......((((((((((((((..((.....))..))))))).)))))))....(((.((((...(((...(((((..(((((((.((..((((((..((((((...))))))..))))))..)))))))))...)))))...)))...))))..(((.((((((..(((((((((.....))).....))))))...(((((....)))))...((((((.((......................((((..(((((......(((((.(((.............)))))))))))))..))))(((((....))))).....))..)))))))))))).)))...))))))))).......((((.....))))..)))..)).))). (-105.72) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 901 100 51 191 142 NC_009009:SSA_1975|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1971132..1971362_NEGATIVE 396 306 270 62 26 NC_009009:SSA_1262|5end_tRNA_modification_GTPase,_possibly_iron-binding,_putative_1287782..1288012_POSITIVE 331 301 269 194 153 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 330 315 273 60 5 NC_009009:SSA_0494|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_494407..494637_POSITIVE 323 279 233 63 14 NC_009009:SSA_1149|5end_Glycosyl_hydrolase,_family_1,_putative_1178399..1178629_POSITIVE 321 280 233 64 5 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 320 299 258 63 5 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 319 289 242 68 3 NC_009009:SSA_1636|5end_ABC-type_antibiotic_exporter,_ATPase_component,_putative_1640905..1641135_NEGATIVE 312 48 3 149 91 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 305 280 233 57 2 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 302 250 202 103 52 NC_009009:SSA_2103|5end_hypothetical_protein_2106700..2106930_NEGATIVE 299 297 253 75 31 NC_009009:SSA_1784|5end_Glutamate_racemase,_putative_1769897..1770127_NEGATIVE 296 59 13 152 104 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 296 281 241 211 172 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 291 313 271 51 8 NC_009009:SSA_0865|5end_hypothetical_protein_856378..856608_POSITIVE 290 306 268 80 27 NC_009009:SSA_0211|5end_hypothetical_protein_208041..208271_POSITIVE 287 317 272 90 33 NC_009009:SSA_1058|5end_Thiamine_biosynthesis_protein,_putative_1074917..1075147_POSITIVE 286 219 171 230 179 NC_009009:SSA_0653|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_636390..636620_POSITIVE 286 289 249 68 27 NC_009009:SSA_0595|5end_hypothetical_protein_586490..586720_POSITIVE 285 335 292 230 183 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 299 251 66 3 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 330 315 273 56 1 NC_009009:SSA_0493|3end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_494483..494633_POSITIVE 323 279 233 57 8 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 322 306 268 40 4 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE 312 48 3 146 88 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 306 294 269 135 104 NC_009009:SSA_1286|3end_hypothetical_protein_1305759..1305909_NEGATIVE 296 59 13 150 102 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE 296 290 241 134 75 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 290 306 268 83 30 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 288 316 271 68 14 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 287 296 253 45 2 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 287 317 272 86 29 NC_009009:SSA_1057|3end_Aminotransferase,_class-V,_putative_1074993..1075143_POSITIVE 286 183 150 145 111 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 283 316 272 72 36 NC_009009:SSA_0481|3end_Cobyric_acid_synthase,_putative_483541..483691_POSITIVE 282 317 271 139 98 NC_009009:SSA_2073|3end_Undecaprenyl_pyrophosphate_synthetase,_putative_2075622..2075772_NEGATIVE 279 317 273 70 12 NC_009009:SSA_0136|3end_ABC_transporter,_Zn_porter,_putative_131804..131954_POSITIVE 278 240 194 96 58 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 276 280 232 77 17 NC_009009:SSA_2219|3end_UDP-glucose_4-epimerase,_putative_2219967..2220117_NEGATIVE 272 66 26 56 16 NC_009009:SSA_0820|3end_Ribosomal_protein_S21,_putative_801505..801655_POSITIVE 268 124 81 121 76 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE