Origin IGS: atataaacctccagatactcattagacaataaattgacatactttattatccattatagcataaatcaaaaatcagagttgcatactaaaaaagaccggtcgcccgatctttcatcttgtattaaaattcttcatctatcttgctatatcgcggttttgctcgcggcctttaatagactcgcgcttggcgtaagtgtcatttgccagtaggttcatgttcccacaatgtcta .........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 tagacattgtgggaacatgaacctactggcaaatgacacttacgccaagcgcgagtctattaaaggccgcgagcaaaaccgcgatatagcaagatagatgaagaattttaatacaagatgaaagatcgggcgaccggtcttttttagtatgcaactctgatttttgatttatgctataatggataataaagtatgtcaatttattgtctaatgagtatctggaggtttatat Mask Tandem Repeat Region ================================================ atataaacctccagatactcattagacaataaattgacatactttattatccattatagcataaatcaaaaatcagagttgcatactaaaaaagaccggtcgcccgatctttcatcttgtattaaaattcttcatctatcttgctatatcgcggttttgctcgcggcctttaatagactcgcgcttggcgtaagtgtcatttgccagtaggttcatgttcccacaatgtcta Find is-nt database================================================ Query_seq: SSA_1596:SSA_1597|SSA_1596:SSA_1597:hypothetical protein:hypothetical protein:<-<-:1603125..1603356 232 atataaacctccagatactcattagacaataaattgacatactttattatccattatagcataaatcaaaaatcagagttgcatactaaaaaagaccggtcgcccgatctttcatcttgtattaaaattcttcatctatcttgctatatcgcggttttgctcgcggcctttaatagactcgcgcttggcgtaagtgtcatttgccagtaggttcatgttcccacaatgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1596:SSA_1597|SSA_1596:SSA_1597:hypothetical protein:hypothetical protein:<-<-:1603125..1603356 232 atataaacctccagatactcattagacaataaattgacatactttattatccattatagcataaatcaaaaatcagagttgcatactaaaaaagaccggtcgcccgatctttcatcttgtattaaaattcttcatctatcttgctatatcgcggttttgctcgcggcctttaatagactcgcgcttggcgtaagtgtcatttgccagtaggttcatgttcccacaatgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1596:SSA_1597|SSA_1596:SSA_1597:hypothetical protein:hypothetical protein:<-<-:1603125..1603356 232 atataaacctccagatactcattagacaataaattgacatactttattatccattatagcataaatcaaaaatcagagttgcatactaaaaaagaccggtcgcccgatctttcatcttgtattaaaattcttcatctatcttgctatatcgcggttttgctcgcggcctttaatagactcgcgcttggcgtaagtgtcatttgccagtaggttcatgttcccacaatgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atataaacctccagatactcattagacaataaattgacatactttattatccattatagcataaatcaaaaatcagagttgcatactaaaaaagaccggtcgcccgatctttcatcttgtattaaaattcttcatctatcttgctatatcgcggttttgctcgcggcctttaatagactcgcgcttggcgtaagtgtcatttgccagtaggttcatgttcccacaatgtcta Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 65 End: 190 ................................................................ M K N Q S C I L K K T G R P I F H L V L K F F I Y L A I S R F C S R P L I D S R L A .......................................... Protein_Len: 58 Strand: + Start: 34 End: 207 ................................. M T Y F I I H Y S I N Q K S E L H T K K D R S P D L S S C I K I L H L S C Y I A V L L A A F N R L A L G V S V I C Q ......................... atataaacctccagatactcattagacaataaattgacatactttattatccattatagcataaatcaaaaatcagagttgcatactaaaaaagaccggtcgcccgatctttcatcttgtattaaaattcttcatctatcttgctatatcgcggttttgctcgcggcctttaatagactcgcgcttggcgtaagtgtcatttgccagtaggttcatgttcccacaatgtcta 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: 86 Start: 33 End: 62 ................................ATTGACATACTTTATTATCCATTATAGCAT.......................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atataaacctccagatactcattagacaataaattgacatactttattatccattatagcataaatcaaaaatcagagttgcatactaaaaaagaccggtcgcccgatctttcatcttgtattaaaattcttcatctatcttgctatatcgcggttttgctcgcggcctttaatagactcgcgcttggcgtaagtgtcatttgccagtaggttcatgttcccacaatgtcta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 86 HP_score: -6.8 Tail_Score: -5.21709 Start: 94 End: 109 Full_Region: taatacaagatgaaa gatcgg gcga ccggtc ttttttagtatgcaa .............................................................................................gatcgggcgaccggtc........................................................................................................................... Find igs database================================================ Query_seq: SSA_1596:SSA_1597|SSA_1596:SSA_1597:hypothetical protein:hypothetical protein:<-<-:1603125..1603356 232 atataaacctccagatactcattagacaataaattgacatactttattatccattatagcataaatcaaaaatcagagttgcatactaaaaaagaccggtcgcccgatctttcatcttgtattaaaattcttcatctatcttgctatatcgcggttttgctcgcggcctttaatagactcgcgcttggcgtaagtgtcatttgccagtaggttcatgttcccacaatgtcta Intra-Species Hit: Count: 1 Min: 1 Max: 232 Len: 232 Subject: NC_009009_SSA_1596_SSA_1597|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1603125,1603356]|232 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 atataaacctccagatactcattagacaataaattgacatactttattatccattatagcataaatcaaaaatcagagttgcatactaaaaaagaccggtcgcccgatctttcatcttgtattaaaattcttcatctatcttgctatatcgcggttttgctcgcggcctttaatagactcgcgcttggcgtaagtgtcatttgccagtaggttcatgttcccacaatgtcta atataaacctccagatactcattagacaataaattgacatactttattatccattatagcataaatcaaaaatcagagttgcatactaaaaaagaccggtcgcccgatctttcatcttgtattaaaattcttcatctatcttgctatatcgcggttttgctcgcggcctttaatagactcgcgcttggcgtaagtgtcatttgccagtaggttcatgttcccacaatgtcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAAACCUCCAGAUACUCAUUAGACAAUAAAUUGACAUACUUUAUUAUCCAUUAUAGCAUAAAUCAAAAAUCAGAGUUGCAUACUAAAAAAGACCGGUCGCCCGAUCUUUCAUCUUGUAUUAAAAUUCUUCAUCUAUCUUGCUAUAUCGCGGUUUUGCUCGCGGCCUUUAAUAGACUCGCGCUUGGCGUAAGUGUCAUUUGCCAGUAGGUUCAUGUUCCCACAAUGUCUA ......................((((((......((((((..(((((((.....(((((((.............((((((..((((....(((((.(((....))).)))))......))))...))))))..........))))))).(((((......))))).....)))))))...((((...))))..)))))).......((.((........)).))..)))))) (-43.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGACAUUGUGGGAACAUGAACCUACUGGCAAAUGACACUUACGCCAAGCGCGAGUCUAUUAAAGGCCGCGAGCAAAACCGCGAUAUAGCAAGAUAGAUGAAGAAUUUUAAUACAAGAUGAAAGAUCGGGCGACCGGUCUUUUUUAGUAUGCAACUCUGAUUUUUGAUUUAUGCUAUAAUGGAUAAUAAAGUAUGUCAAUUUAUUGUCUAAUGAGUAUCUGGAGGUUUAUAU ........(((((........))))).(((.............)))...((((.((((.....))))))))....(((((....(((((((...(((((.(((((((...((((.....((((((((((....))))))))))...))))........))))))).)))))))))))).(((((((((((.........))))))))))).............))))).... (-61.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 901 120 71 211 162 NC_009009:SSA_1596|5end_hypothetical_protein_1603034..1603264_NEGATIVE 724 120 71 96 47 NC_009009:SSA_1600|5end_hypothetical_protein_1606595..1606825_NEGATIVE 598 167 121 228 182 NC_009009:SSA_1598|5end_hypothetical_protein_1605238..1605468_NEGATIVE 391 196 151 225 171 NC_009009:SSA_2137|5end_hypothetical_protein_2138412..2138642_NEGATIVE 390 200 151 231 170 NC_009009:SSA_2084|5end_Phosphotransferase_system_(PTS),_galactitol-specific_IIC_component,_putative_2089424..2089654_NEGATIVE 364 189 142 212 160 NC_009009:SSA_1850|5end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1846024..1846254_NEGATIVE 362 190 147 71 19 NC_009009:SSA_1745|5end_General_stress_response_protein_CsbD,_putative_1732191..1732421_NEGATIVE 362 187 143 174 122 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 350 190 143 203 142 NC_009009:SSA_2042|5end_hypothetical_protein_2047073..2047303_NEGATIVE 345 189 151 161 122 NC_009009:SSA_1560|5end_Structural_maintenance_of_chromosome_protein_(chromosome_segregation_ATPase),_putative_1565194..1565424_NEGATIVE 339 215 172 229 168 NC_009009:SSA_1155|5end_Serine_hydroxymethyltransferase,_putative_1183298..1183528_POSITIVE 335 180 133 139 89 NC_009009:SSA_2161|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160600..2160830_NEGATIVE 335 208 163 77 37 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 333 199 151 151 105 NC_009009:SSA_1485|5end_Citrulline_cluster-linked_gene,_putative_1492809..1493039_NEGATIVE 333 190 141 161 108 NC_009009:SSA_0871|5end_Cell_division_protein_FtsX,_putative_863621..863851_POSITIVE 325 190 141 44 2 NC_009009:SSA_1027|5end_hypothetical_protein_1043527..1043757_POSITIVE 321 76 41 231 195 NC_009009:SSA_1599|5end_hypothetical_protein_1606416..1606646_NEGATIVE 320 220 176 49 8 NC_009009:SSA_1607|5end_Formamidopyrimidine-DNA_glycosylase,_putative_1613255..1613485_NEGATIVE 315 189 149 171 122 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 312 190 141 227 168 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 724 120 71 99 50 NC_009009:SSA_1601|3end_VacB-like_protein,_putative_1606592..1606742_NEGATIVE 478 181 144 38 1 NC_009009:SSA_1599|3end_hypothetical_protein_1605442..1605592_NEGATIVE 337 77 41 151 114 NC_009009:SSA_1600|3end_hypothetical_protein_1606497..1606647_NEGATIVE 325 190 141 54 12 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 311 221 181 69 28 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 305 192 152 141 99 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 301 206 161 86 30 NC_009009:SSA_2109|3end_Elongation_factor_G,_putative_2112787..2112937_NEGATIVE 301 190 141 138 85 NC_009009:SSA_1695|3end_Transcriptional_antiterminator,_BglG/SacY_family_(induction_of_sugar_metabolism),_putative_1687177..1687327_NEGATIVE 301 190 146 73 24 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 300 221 187 97 62 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 299 190 143 148 86 NC_009009:SSA_1569|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1572630..1572780_POSITIVE 299 120 74 138 94 NC_009009:SSA_0402|3end_Histidine_kinase,_putative_400099..400249_POSITIVE 297 189 141 149 91 NC_009009:SSA_1151|3end_Thymidine_kinase,_putative_1180802..1180952_POSITIVE 297 225 181 74 38 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 295 210 165 86 42 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 292 163 126 145 107 NC_009009:SSA_1303|3end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322474..1322624_NEGATIVE 290 200 152 123 55 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 289 209 163 65 9 NC_009009:SSA_1641|3end_MutT/nudix_family_protein,_putative_1642543..1642693_NEGATIVE 288 190 152 51 14 NC_009009:SSA_2130|3end_hypothetical_protein_2134020..2134170_POSITIVE 287 189 149 99 65 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE