Origin IGS: agcattacctcgcttttttcatattttgctttacataatttttatttttaccaaagtttcagataagaaatctcttccttatctactataaattttcatttgggagatcttctcctatctattattttacataacttatttcattttcaaaaatcaagactgaatcagtccctgcttttatgagtgaaattgatctctttcagaagaagataattttacataacttttaatcctcccaaaaataattgccttccggctgtattcataccttctgattaaatttacgtaaacttttttgtttacagttgtaattttatcatgacagaatttatttgtcaatagattttacataattttttaaaataaatttacaaatgtaatcgagaaagtcgttgaggtccttttcgttcctataaagacgcttttttataataaaaatctggacataatccagattt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatctggattatgtccagatttttattataaaaaagcgtctttataggaacgaaaaggacctcaacgactttctcgattacatttgtaaatttattttaaaaaattatgtaaaatctattgacaaataaattctgtcatgataaaattacaactgtaaacaaaaaagtttacgtaaatttaatcagaaggtatgaatacagccggaaggcaattatttttgggaggattaaaagttatgtaaaattatcttcttctgaaagagatcaatttcactcataaaagcagggactgattcagtcttgatttttgaaaatgaaataagttatgtaaaataatagataggagaagatctcccaaatgaaaatttatagtagataaggaagagatttcttatctgaaactttggtaaaaataaaaattatgtaaagcaaaatatgaaaaaagcgaggtaatgct Mask Tandem Repeat Region ================================================ agcattacctcgcttttttcatattttgctttacataatttttatttttaccaaagtttcagataagaaatctcttccttatctactataaattttcatttgggagatcttctcctatctattattttacataacttatttcattttcaaaaatcaagactgaatcagtccctgcttttatgagtgaaattgatctctttcagaagaagataattttacataacttttaatcctcccaaaaataattgccttccggctgtattcataccttctgattaaatttacgtaaacttttttgtttacagttgtaattttatcatgacagaatttatttgtcaatagattttacataattttttaaaataaatttacaaatgtaatcgagaaagtcgttgaggtccttttcgttcctataaagacgcttttttataataaaaatctggacataatccagattt Find is-nt database================================================ Query_seq: SSA_2096:SSA_2097|SSA_2096:SSA_2097:ATP-dependent protease, ATP-binding subunit, putative:Amino acid ABC transporter, ATP-binding protein, putative:<-<-:2101786..2102243 458 agcattacctcgcttttttcatattttgctttacataatttttatttttaccaaagtttcagataagaaatctcttccttatctactataaattttcatttgggagatcttctcctatctattattttacataacttatttcattttcaaaaatcaagactgaatcagtccctgcttttatgagtgaaattgatctctttcagaagaagataattttacataacttttaatcctcccaaaaataattgccttccggctgtattcataccttctgattaaatttacgtaaacttttttgtttacagttgtaattttatcatgacagaatttatttgtcaatagattttacataattttttaaaataaatttacaaatgtaatcgagaaagtcgttgaggtccttttcgttcctataaagacgcttttttataataaaaatctggacataatccagattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2096:SSA_2097|SSA_2096:SSA_2097:ATP-dependent protease, ATP-binding subunit, putative:Amino acid ABC transporter, ATP-binding protein, putative:<-<-:2101786..2102243 458 agcattacctcgcttttttcatattttgctttacataatttttatttttaccaaagtttcagataagaaatctcttccttatctactataaattttcatttgggagatcttctcctatctattattttacataacttatttcattttcaaaaatcaagactgaatcagtccctgcttttatgagtgaaattgatctctttcagaagaagataattttacataacttttaatcctcccaaaaataattgccttccggctgtattcataccttctgattaaatttacgtaaacttttttgtttacagttgtaattttatcatgacagaatttatttgtcaatagattttacataattttttaaaataaatttacaaatgtaatcgagaaagtcgttgaggtccttttcgttcctataaagacgcttttttataataaaaatctggacataatccagattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2096:SSA_2097|SSA_2096:SSA_2097:ATP-dependent protease, ATP-binding subunit, putative:Amino acid ABC transporter, ATP-binding protein, putative:<-<-:2101786..2102243 458 agcattacctcgcttttttcatattttgctttacataatttttatttttaccaaagtttcagataagaaatctcttccttatctactataaattttcatttgggagatcttctcctatctattattttacataacttatttcattttcaaaaatcaagactgaatcagtccctgcttttatgagtgaaattgatctctttcagaagaagataattttacataacttttaatcctcccaaaaataattgccttccggctgtattcataccttctgattaaatttacgtaaacttttttgtttacagttgtaattttatcatgacagaatttatttgtcaatagattttacataattttttaaaataaatttacaaatgtaatcgagaaagtcgttgaggtccttttcgttcctataaagacgcttttttataataaaaatctggacataatccagattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcattacctcgcttttttcatattttgctttacataatttttatttttaccaaagtttcagataagaaatctcttccttatctactataaattttcatttgggagatcttctcctatctattattttacataacttatttcattttcaaaaatcaagactgaatcagtccctgcttttatgagtgaaattgatctctttcagaagaagataattttacataacttttaatcctcccaaaaataattgccttccggctgtattcataccttctgattaaatttacgtaaacttttttgtttacagttgtaattttatcatgacagaatttatttgtcaatagattttacataattttttaaaataaatttacaaatgtaatcgagaaagtcgttgaggtccttttcgttcctataaagacgcttttttataataaaaatctggacataatccagattt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 70 End: 180 ..................................................................... M S S L S T I N F H L G D L L L S I I L H N L F H F Q K S R L N Q S L L L ...................................................................................................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 138 End: 227 ......................................................................................................................................... M S F S K I K T E S V P A F M S E I D L F Q K K I I L H N F ....................................................................................................................................................................................................................................... Protein_Len: 41 Strand: - Start: 332 End: 454 ........................................................................................................................................................................................................................................................................................................................................... K D I S K V Y N K L I F K C I Y D L F D N L D K E N R Y L R K K I I F I Q V Y D M .... Protein_Len: 53 Strand: - Start: 181 End: 339 .................................................................................................................................................................................... S H F Q D R E S S S L K V Y S K I R G F I I A K R S Y E Y R R I L N V Y V K K N V T T I K D H C F K N T M ....................................................................................................................... agcattacctcgcttttttcatattttgctttacataatttttatttttaccaaagtttcagataagaaatctcttccttatctactataaattttcatttgggagatcttctcctatctattattttacataacttatttcattttcaaaaatcaagactgaatcagtccctgcttttatgagtgaaattgatctctttcagaagaagataattttacataacttttaatcctcccaaaaataattgccttccggctgtattcataccttctgattaaatttacgtaaacttttttgtttacagttgtaattttatcatgacagaatttatttgtcaatagattttacataattttttaaaataaatttacaaatgtaatcgagaaagtcgttgaggtccttttcgttcctataaagacgcttttttataataaaaatctggacataatccagattt 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: 91 Start: 311 End: 340 ......................................................................................................................................................................................................................................................................................................................ATTGACAAATAAATTCTGTCATGATAAAAT...................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 214 End: 243 .....................................................................................................................................................................................................................TTTTACATAACTTTTAATCCTCCCAAAAAT....................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcattacctcgcttttttcatattttgctttacataatttttatttttaccaaagtttcagataagaaatctcttccttatctactataaattttcatttgggagatcttctcctatctattattttacataacttatttcattttcaaaaatcaagactgaatcagtccctgcttttatgagtgaaattgatctctttcagaagaagataattttacataacttttaatcctcccaaaaataattgccttccggctgtattcataccttctgattaaatttacgtaaacttttttgtttacagttgtaattttatcatgacagaatttatttgtcaatagattttacataattttttaaaataaatttacaaatgtaatcgagaaagtcgttgaggtccttttcgttcctataaagacgcttttttataataaaaatctggacataatccagattt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -7.7 Tail_Score: -3.81256 Start: 158 End: 170 Full_Region: actcataaaagcagg gactg att cagtc ttgatttttgaaaat .............................................................................................................................................................gactgattcagtc................................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 40 HP_score: -2.9 Tail_Score: -2.67803 Start: 285 End: 304 Full_Region: tgataaaattacaac tgtaaac aaaaaa gtttacg taaatttaatcagaa ............................................................................................................................................................................................................................................................................................tgtaaacaaaaaagtttacg.......................................................................................................................................................... Find igs database================================================ Query_seq: SSA_2096:SSA_2097|SSA_2096:SSA_2097:ATP-dependent protease, ATP-binding subunit, putative:Amino acid ABC transporter, ATP-binding protein, putative:<-<-:2101786..2102243 458 agcattacctcgcttttttcatattttgctttacataatttttatttttaccaaagtttcagataagaaatctcttccttatctactataaattttcatttgggagatcttctcctatctattattttacataacttatttcattttcaaaaatcaagactgaatcagtccctgcttttatgagtgaaattgatctctttcagaagaagataattttacataacttttaatcctcccaaaaataattgccttccggctgtattcataccttctgattaaatttacgtaaacttttttgtttacagttgtaattttatcatgacagaatttatttgtcaatagattttacataattttttaaaataaatttacaaatgtaatcgagaaagtcgttgaggtccttttcgttcctataaagacgcttttttataataaaaatctggacataatccagattt Intra-Species Hit: Count: 1 Min: 50 Max: 458 Len: 409 Subject: NC_009009_SSA_2096_SSA_2097|ATP-dependent protease, ATP-binding subunit, putative:Amino acid ABC transporter, ATP-binding protein, putative|NEGATIVE:NEGATIVE|[2101786,2102243]|458 HSP 1 e-value: 0.0 bit: 811.0 Len: 409 Query Start:50 Query End:458 Subject Strand: POSITIVE Subject Start: 50 Subject End: 458 .................................................accaaagtttcagataagaaatctcttccttatctactataaattttcatttgggagatcttctcctatctattattttacataacttatttcattttcaaaaatcaagactgaatcagtccctgcttttatgagtgaaattgatctctttcagaagaagataattttacataacttttaatcctcccaaaaataattgccttccggctgtattcataccttctgattaaatttacgtaaacttttttgtttacagttgtaattttatcatgacagaatttatttgtcaatagattttacataattttttaaaataaatttacaaatgtaatcgagaaagtcgttgaggtccttttcgttcctataaagacgcttttttataataaaaatctggacataatccagattt .................................................accaaagtttcagataagaaatctcttccttatctactataaattttcatttgggagatcttctcctatctattattttacataacttatttcattttcaaaaatcaagactgaatcagtccctgcttttatgagtgaaattgatctctttcagaagaagataattttacataacttttaatcctcccaaaaataattgccttccggctgtattcataccttctgattaaatttacgtaaacttttttgtttacagttgtaattttatcatgacagaatttatttgtcaatagattttacataattttttaaaataaatttacaaatgtaatcgagaaagtcgttgaggtccttttcgttcctataaagacgcttttttataataaaaatctggacataatccagattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCAAAGUUUCAGAUAAGAAAUCUCUUCCUUAUCUACUAUAAAUUUUCAUUUGGGAGAUCUUCUCCUAUCUAUUAUUUUACAUAACUUAUUUCAUUUUCAAAAAUCAAGACUGAAUCAGUCCCUGCUUUUAUGAGUGAAAUUGAUCUCUUUCAGAAGAAGAUAAUUUUACAUAACUUUUAAUCCUCCCAAAAAUAAUUGCCUUCCGGCUGUAUUCAUACCUUCUGAUUAAAUUUACGUAAACUUUUUUGUUUACAGUUGUAAUUUUAUCAUGACAGAAUUUAUUUGUCAAUAGAUUUUACAUAAUUUUUUAAAAUAAAUUUACAAAUGUAAUCGAGAAAGUCGUUGAGGUCCUUUUCGUUCCUAUAAAGACGCUUUUUUAUAAUAAAAAUCUGGACAUAAUCCAGAUUU ....(((((..(((((((..........)))))))....((((........((((((.....))))))........))))...))))).((((((((...((((.((.(((((...)))))..)).))))..))))))))..((((((..(((((((..(((..................)))........((((...(((....)))..)))).....)))))))........(((...(((((((((.(((((.((((((.(((((..(((((((.....)))))))..(((((......)))))......))))).)))))).))))).)))))))))))).))))))...........((((((((....))))))))....(((((((((.....))))))))) (-82.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCUGGAUUAUGUCCAGAUUUUUAUUAUAAAAAAGCGUCUUUAUAGGAACGAAAAGGACCUCAACGACUUUCUCGAUUACAUUUGUAAAUUUAUUUUAAAAAAUUAUGUAAAAUCUAUUGACAAAUAAAUUCUGUCAUGAUAAAAUUACAACUGUAAACAAAAAAGUUUACGUAAAUUUAAUCAGAAGGUAUGAAUACAGCCGGAAGGCAAUUAUUUUUGGGAGGAUUAAAAGUUAUGUAAAAUUAUCUUCUUCUGAAAGAGAUCAAUUUCACUCAUAAAAGCAGGGACUGAUUCAGUCUUGAUUUUUGAAAAUGAAAUAAGUUAUGUAAAAUAAUAGAUAGGAGAAGAUCUCCCAAAUGAAAAUUUAUAGUAGAUAAGGAAGAGAUUUCUUAUCUGAAACUUUGGU ((((((((((...)))))))))).(((((((((.....((((((...........)))))).(((...(((((((.(((((.(((((.....................(((((.(((...(((((.........))))).)))....)))))...((((((......)))))).))))).)))))))))))).))).....(((....))).......((((((((.......((((......)))).((((((((((..........((((((....((((((..(((((((...)))))))..))))))....))))))..(((((.....)))))...)))))))))).))))))))......)))))))))(((((((((....)))))))))............ (-95.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 793 70 21 210 161 NC_009009:SSA_2096|5end_ATP-dependent_protease,_ATP-binding_subunit,_putative_2101695..2101925_NEGATIVE 290 377 342 81 35 NC_009009:SSA_0663|5end_Acetyltransferase,_putative_648352..648582_POSITIVE 290 378 332 134 73 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 288 225 182 136 99 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 282 67 21 102 60 NC_009009:SSA_1842|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_HTH_DNA-binding_domains),_putative_1836494..1836724_NEGATIVE 277 250 205 124 79 NC_009009:SSA_0860|5end_N-acetylmuramidase/lysin,_putative_847615..847845_POSITIVE 275 136 93 179 131 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 271 368 339 76 47 NC_009009:SSA_1848|5end_Methionyl-tRNA_formyltransferase,_putative_1843178..1843408_NEGATIVE 271 219 175 139 95 NC_009009:SSA_1037|5end_Cytidine_deaminase,_putative_1052118..1052348_POSITIVE 263 372 334 231 192 NC_009009:SSA_1666|5end_Collagen-binding_surface_protein,_putative_1667312..1667542_NEGATIVE 263 150 106 61 7 NC_009009:SSA_1130|5end_Iron-dependent_peroxidase,_putative_1155802..1156032_POSITIVE 260 220 173 167 117 NC_009009:SSA_2221|5end_Cps9E,_putative_2223257..2223487_NEGATIVE 259 228 181 191 132 NC_009009:SSA_1492|5end_hypothetical_protein_1498954..1499184_NEGATIVE 257 170 121 88 35 NC_009009:SSA_2106|5end_Flavin_monoxygenase,_putative_2109064..2109294_NEGATIVE 257 156 111 42 5 NC_009009:SSA_1579|5end_ABC-type_Fe3+-siderophore_transport_system,_ATPase_component,_putative_1582851..1583081_POSITIVE 256 80 33 112 68 NC_009009:SSA_1943|5end_Aspartate_kinase,_putative_1928697..1928927_POSITIVE 256 149 107 201 144 NC_009009:SSA_1423|5end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1433783..1434013_NEGATIVE 253 381 342 91 49 NC_009009:SSA_0030|5end_Phosphoribosylformylglycinamidine_synthase,_putative_32610..32840_POSITIVE 252 226 182 64 17 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 252 375 331 150 113 NC_009009:SSA_0353|5end_Conserved_uncharacterized_protein_345940..346170_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 216 173 135 86 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 288 225 182 134 97 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE 282 67 21 124 82 NC_009009:SSA_1843|3end_Histidine_kinase,_putative_1836472..1836622_NEGATIVE 277 378 333 102 53 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 272 209 178 134 98 NC_009009:SSA_0040|3end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_47479..47629_POSITIVE 263 150 106 56 2 NC_009009:SSA_1129|3end_Periplasmic_iron_transport_lipoprotein,_putative_1155877..1156027_POSITIVE 261 227 184 150 114 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 260 220 173 125 75 NC_009009:SSA_2222|3end_Tyrosine-protein_kinase_Wze,_putative_2223299..2223449_NEGATIVE 257 156 111 40 3 NC_009009:SSA_1578|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1582929..1583079_POSITIVE 256 149 107 95 38 NC_009009:SSA_1424|3end_Hydrolase,_putative_1433889..1434039_NEGATIVE 254 162 121 140 97 NC_009009:SSA_2014|3end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014019..2014169_NEGATIVE 253 381 342 71 29 NC_009009:SSA_0028|3end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_32670..32820_POSITIVE 252 226 182 77 30 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 251 226 182 141 95 NC_009009:SSA_0245|3end_hypothetical_protein_239608..239758_POSITIVE 248 190 145 80 26 NC_009009:SSA_2219|3end_UDP-glucose_4-epimerase,_putative_2219967..2220117_NEGATIVE 245 224 181 61 7 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 245 135 104 79 46 NC_009009:SSA_0368|3end_hypothetical_protein_359722..359872_POSITIVE 244 377 333 70 32 NC_009009:SSA_1453|3end_hypothetical_protein_1459897..1460047_NEGATIVE 240 375 333 47 3 NC_009009:SSA_0932|3end_hypothetical_protein_942804..942954_POSITIVE 238 99 51 112 64 NC_009009:SSA_1897|3end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894154..1894304_NEGATIVE