Origin IGS: aacgttacttctgatttcctatattttagaaaccagcccttcttattaaaaattggtatagtatacttgaagttaaataacttcaacaaagatagtatacacactgttttttggtttgtcaagtataaaattggtatagttttctttaagaaaactatgcttagcttctattaccgcaaaacagccccttgaagcatttagaaaaatggacagatgtatcagaactgactttctatataactaataaagaataggaaatagagctgtacattcgctctgtctctaataattctcgcaaaacagtgcacagaaaaagagactcaaatgagcctctttcttctactattgaa .........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 ttcaatagtagaagaaagaggctcatttgagtctctttttctgtgcactgttttgcgagaattattagagacagagcgaatgtacagctctatttcctattctttattagttatatagaaagtcagttctgatacatctgtccatttttctaaatgcttcaaggggctgttttgcggtaatagaagctaagcatagttttcttaaagaaaactataccaattttatacttgacaaaccaaaaaacagtgtgtatactatctttgttgaagttatttaacttcaagtatactataccaatttttaataagaagggctggtttctaaaatataggaaatcagaagtaacgtt Mask Tandem Repeat Region ================================================ aacgttacttctgatttcctatattttagaaaccagcccttcttattaaaaattggtatagtatacttgaagttaaataacttcaacaaagatagtatacacactgttttttggtttgtcaagtataaaattggtatagttttctttaagaaaactatgcttagcttctattaccgcaaaacagccccttgaagcatttagaaaaatggacagatgtatcagaactgactttctatataactaataaagaataggaaatagagctgtacattcgctctgtctctaataattctcgcaaaacagtgcacagaaaaagagactcaaatgagcctctttcttctactattgaa Find is-nt database================================================ Query_seq: SSA_2107:SSA_2108|SSA_2107:SSA_2108:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing], putative:Glyceraldehyde 3-phosphate dehydrogenase, putative:<-<-:2111197..2111546 350 aacgttacttctgatttcctatattttagaaaccagcccttcttattaaaaattggtatagtatacttgaagttaaataacttcaacaaagatagtatacacactgttttttggtttgtcaagtataaaattggtatagttttctttaagaaaactatgcttagcttctattaccgcaaaacagccccttgaagcatttagaaaaatggacagatgtatcagaactgactttctatataactaataaagaataggaaatagagctgtacattcgctctgtctctaataattctcgcaaaacagtgcacagaaaaagagactcaaatgagcctctttcttctactattgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2107:SSA_2108|SSA_2107:SSA_2108:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing], putative:Glyceraldehyde 3-phosphate dehydrogenase, putative:<-<-:2111197..2111546 350 aacgttacttctgatttcctatattttagaaaccagcccttcttattaaaaattggtatagtatacttgaagttaaataacttcaacaaagatagtatacacactgttttttggtttgtcaagtataaaattggtatagttttctttaagaaaactatgcttagcttctattaccgcaaaacagccccttgaagcatttagaaaaatggacagatgtatcagaactgactttctatataactaataaagaataggaaatagagctgtacattcgctctgtctctaataattctcgcaaaacagtgcacagaaaaagagactcaaatgagcctctttcttctactattgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2107:SSA_2108|SSA_2107:SSA_2108:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing], putative:Glyceraldehyde 3-phosphate dehydrogenase, putative:<-<-:2111197..2111546 350 aacgttacttctgatttcctatattttagaaaccagcccttcttattaaaaattggtatagtatacttgaagttaaataacttcaacaaagatagtatacacactgttttttggtttgtcaagtataaaattggtatagttttctttaagaaaactatgcttagcttctattaccgcaaaacagccccttgaagcatttagaaaaatggacagatgtatcagaactgactttctatataactaataaagaataggaaatagagctgtacattcgctctgtctctaataattctcgcaaaacagtgcacagaaaaagagactcaaatgagcctctttcttctactattgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacgttacttctgatttcctatattttagaaaccagcccttcttattaaaaattggtatagtatacttgaagttaaataacttcaacaaagatagtatacacactgttttttggtttgtcaagtataaaattggtatagttttctttaagaaaactatgcttagcttctattaccgcaaaacagccccttgaagcatttagaaaaatggacagatgtatcagaactgactttctatataactaataaagaataggaaatagagctgtacattcgctctgtctctaataattctcgcaaaacagtgcacagaaaaagagactcaaatgagcctctttcttctactattgaa Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 52 End: 189 ................................................... M G I V Y L K L N N F N K D S I H T V F W F V K Y K I G I V F F K K T M L S F Y Y R K T A P ................................................................................................................................................................. Protein_Len: 31 Strand: + Start: 258 End: 350 ................................................................................................................................................................................................................................................................. M E L Y I R S V S N N S R K T V H R K R D S N E P L S S T I E Protein_Len: 37 Strand: - Start: 236 End: 346 ........................................................................................................................................................................................................................................... I V L L S Y S I S S Y M R E T E L L E R L V T C L F L S E F S G R E E V M .... Protein_Len: 49 Strand: - Start: 76 End: 222 ........................................................................... I V E V F I T Y V S N K P K D L I F N T Y N E K L F S H K A E I V A F C G R S A N L F I S L H I M ................................................................................................................................ Protein_Len: 52 Strand: - Start: 3 End: 158 .. T V E S K R Y K L F W G K K N F I P I T Y K F N F L K L L S L I C V T K Q N T L Y L I P I T K K L F V M ................................................................................................................................................................................................ aacgttacttctgatttcctatattttagaaaccagcccttcttattaaaaattggtatagtatacttgaagttaaataacttcaacaaagatagtatacacactgttttttggtttgtcaagtataaaattggtatagttttctttaagaaaactatgcttagcttctattaccgcaaaacagccccttgaagcatttagaaaaatggacagatgtatcagaactgactttctatataactaataaagaataggaaatagagctgtacattcgctctgtctctaataattctcgcaaaacagtgcacagaaaaagagactcaaatgagcctctttcttctactattgaa 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: 87 Start: 94 End: 123 .............................................................................................CTTGACAAACCAAAAAACAGTGTGTATACT................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacgttacttctgatttcctatattttagaaaccagcccttcttattaaaaattggtatagtatacttgaagttaaataacttcaacaaagatagtatacacactgttttttggtttgtcaagtataaaattggtatagttttctttaagaaaactatgcttagcttctattaccgcaaaacagccccttgaagcatttagaaaaatggacagatgtatcagaactgactttctatataactaataaagaataggaaatagagctgtacattcgctctgtctctaataattctcgcaaaacagtgcacagaaaaagagactcaaatgagcctctttcttctactattgaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -11.8 Tail_Score: -3.29147 Start: 134 End: 160 Full_Region: TCAAGTATAAAATTG GTATAGTTTTCT TTA AGAAAACTATGC TTAGCTTCTATTACC .....................................................................................................................................GTATAGTTTTCTTTAAGAAAACTATGC.............................................................................................................................................................................................. Find igs database================================================ Query_seq: SSA_2107:SSA_2108|SSA_2107:SSA_2108:Glucosamine--fructose-6-phosphate aminotransferase [isomerizing], putative:Glyceraldehyde 3-phosphate dehydrogenase, putative:<-<-:2111197..2111546 350 aacgttacttctgatttcctatattttagaaaccagcccttcttattaaaaattggtatagtatacttgaagttaaataacttcaacaaagatagtatacacactgttttttggtttgtcaagtataaaattggtatagttttctttaagaaaactatgcttagcttctattaccgcaaaacagccccttgaagcatttagaaaaatggacagatgtatcagaactgactttctatataactaataaagaataggaaatagagctgtacattcgctctgtctctaataattctcgcaaaacagtgcacagaaaaagagactcaaatgagcctctttcttctactattgaa Intra-Species Hit: Count: 1 Min: 1 Max: 350 Len: 350 Subject: NC_009009_SSA_2107_SSA_2108|Glucosamine--fructose-6-phosphate aminotransferase [isomerizing], putative:Glyceraldehyde 3-phosphate dehydrogenase, putative|NEGATIVE:NEGATIVE|[2111197,2111546]|350 HSP 1 e-value: 0.0 bit: 694.0 Len: 350 Query Start:1 Query End:350 Subject Strand: POSITIVE Subject Start: 1 Subject End: 350 aacgttacttctgatttcctatattttagaaaccagcccttcttattaaaaattggtatagtatacttgaagttaaataacttcaacaaagatagtatacacactgttttttggtttgtcaagtataaaattggtatagttttctttaagaaaactatgcttagcttctattaccgcaaaacagccccttgaagcatttagaaaaatggacagatgtatcagaactgactttctatataactaataaagaataggaaatagagctgtacattcgctctgtctctaataattctcgcaaaacagtgcacagaaaaagagactcaaatgagcctctttcttctactattgaa aacgttacttctgatttcctatattttagaaaccagcccttcttattaaaaattggtatagtatacttgaagttaaataacttcaacaaagatagtatacacactgttttttggtttgtcaagtataaaattggtatagttttctttaagaaaactatgcttagcttctattaccgcaaaacagccccttgaagcatttagaaaaatggacagatgtatcagaactgactttctatataactaataaagaataggaaatagagctgtacattcgctctgtctctaataattctcgcaaaacagtgcacagaaaaagagactcaaatgagcctctttcttctactattgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGUUACUUCUGAUUUCCUAUAUUUUAGAAACCAGCCCUUCUUAUUAAAAAUUGGUAUAGUAUACUUGAAGUUAAAUAACUUCAACAAAGAUAGUAUACACACUGUUUUUUGGUUUGUCAAGUAUAAAAUUGGUAUAGUUUUCUUUAAGAAAACUAUGCUUAGCUUCUAUUACCGCAAAACAGCCCCUUGAAGCAUUUAGAAAAAUGGACAGAUGUAUCAGAACUGACUUUCUAUAUAACUAAUAAAGAAUAGGAAAUAGAGCUGUACAUUCGCUCUGUCUCUAAUAAUUCUCGCAAAACAGUGCACAGAAAAAGAGACUCAAAUGAGCCUCUUUCUUCUACUAUUGAA ...((((.(((((((.((.(((((((.(.((((((............(((((((((((((.(((..((((((((....)))))))).....))).))))).))..)))))))))))).).))))))).....((((((((((((.....))))))))))))..(((((.......((......)).....))))).................))...))))))).))))..................(((((.(((.(((((((.........))))))).)))....))))).......(((((...((((((((((.(((....))).)))))).))))..))))).. (-80.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAUAGUAGAAGAAAGAGGCUCAUUUGAGUCUCUUUUUCUGUGCACUGUUUUGCGAGAAUUAUUAGAGACAGAGCGAAUGUACAGCUCUAUUUCCUAUUCUUUAUUAGUUAUAUAGAAAGUCAGUUCUGAUACAUCUGUCCAUUUUUCUAAAUGCUUCAAGGGGCUGUUUUGCGGUAAUAGAAGCUAAGCAUAGUUUUCUUAAAGAAAACUAUACCAAUUUUAUACUUGACAAACCAAAAAACAGUGUGUAUACUAUCUUUGUUGAAGUUAUUUAACUUCAAGUAUACUAUACCAAUUUUUAAUAAGAAGGGCUGGUUUCUAAAAUAUAGGAAAUCAGAAGUAACGUU ..(((..((((.((((((((((((....)))))))))))).((..(((((((((.((((.....(((((((..(..((.((((((((..((((((.((((.((.....))....)))).)))).))..))).))))).))..)...)))))))..(((((.....((((.....))))....))))).....(((((((((.....)))))))))............)))).........)))))))))..))..))))..))).(((((((....))))))).((.((((...((..((((....))))..))(((((((((........))))))))).))))))... (-88.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 762 50 1 141 92 NC_009009:SSA_2107|5end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2111106..2111336_NEGATIVE 319 280 246 71 37 NC_009009:SSA_1135|5end_Na+-driven_multidrug_efflux_pump,_putative_1160352..1160582_POSITIVE 305 310 261 180 130 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 303 297 254 148 101 NC_009009:SSA_2275|5end_hypothetical_protein_2275590..2275820_NEGATIVE 303 308 261 130 82 NC_009009:SSA_1719|5end_Conserved_uncharacterized_protein_1706793..1707023_NEGATIVE 302 200 155 214 172 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 280 305 261 219 174 NC_009009:SSA_2231|5end_Heme/copper-type_cytochrome/quinol_oxidases,_subunit_1,_putative_2232928..2233158_NEGATIVE 280 285 253 163 135 NC_009009:SSA_0818|5end_SPX_domain-like_protein,_putative_799675..799905_POSITIVE 273 196 161 229 189 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 269 190 145 120 75 NC_009009:SSA_2333|5end_Integral_membrane_protein,_putative_2336460..2336690_NEGATIVE 268 300 259 230 180 NC_009009:SSA_0938|5end_hypothetical_protein_946587..946817_POSITIVE 268 218 172 203 157 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 267 306 261 61 16 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 264 338 292 116 72 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 262 229 181 73 22 NC_009009:SSA_0378|5end_TRZ/ATZ_family_hydrolase,_putative_367276..367506_POSITIVE 259 237 200 86 48 NC_009009:SSA_1751|5end_Dextran_glucosidase,_alpha_amylase_family,_putative_1739801..1740031_NEGATIVE 257 225 182 176 124 NC_009009:SSA_1120|5end_Two-component_sensor_kinase_(with_C-terminal_ATPase_domain),_putative_1145222..1145452_POSITIVE 255 309 262 59 2 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 255 177 131 144 85 NC_009009:SSA_2076|5end_Conserved_uncharacterized_protein_2080481..2080711_NEGATIVE 253 190 159 200 154 NC_009009:SSA_0758|5end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_740636..740866_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 306 261 52 4 NC_009009:SSA_2367|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368845..2368995_NEGATIVE 303 297 254 151 104 NC_009009:SSA_2276|3end_hypothetical_protein_2275587..2275737_NEGATIVE 303 308 261 127 79 NC_009009:SSA_1720|3end_Initiation-control_protein,_putative_1706796..1706946_NEGATIVE 301 188 149 110 60 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 301 195 158 53 11 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 278 344 302 79 32 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 269 190 145 123 78 NC_009009:SSA_2334|3end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2336457..2336607_NEGATIVE 264 196 152 143 101 NC_009009:SSA_0815|3end_hypothetical_protein_797411..797561_POSITIVE 259 237 200 75 37 NC_009009:SSA_1752|3end_Phosphotransferase_system,_trehalose-specific_IIBC_component,_putative_1739812..1739962_NEGATIVE 256 296 261 146 114 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 249 68 28 67 25 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 249 195 158 121 88 NC_009009:SSA_0362|3end_Thioredoxin,_putative_353594..353744_POSITIVE 246 197 154 47 6 NC_009009:SSA_0984|3end_SlyA-like_protein,_putative_987571..987721_POSITIVE 242 194 158 124 92 NC_009009:SSA_0141|3end_Copper_chaperone,_putative_137191..137341_POSITIVE 241 296 261 48 13 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 238 230 189 102 57 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 238 310 267 130 79 NC_009009:SSA_1198|3end_ATPase_(PilT_family),_putative_1222703..1222853_NEGATIVE 238 284 248 128 93 NC_009009:SSA_0887|3end_hypothetical_protein_881165..881315_NEGATIVE 238 230 182 91 51 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 238 214 171 136 91 NC_009009:SSA_0149|3end_hypothetical_protein_143833..143983_POSITIVE