Origin IGS: ttttctttgaagtttataacagcgacagaacttagtctcagactaggttctgttttttcttctagcagactcaagaagtgattttgaggtgcgtgctctggtggagaaagagctggcttgaagatgcgggtgggaaatgataatgagaagaattttccacagatcttatccccttaaaataaagatgtttcaatttgatgaaattctgtggataacctttattatttcattcaactatgttacaatgttactataaataaaatagaagaggtgt .........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 acacctcttctattttatttatagtaacattgtaacatagttgaatgaaataataaaggttatccacagaatttcatcaaattgaaacatctttattttaaggggataagatctgtggaaaattcttctcattatcatttcccacccgcatcttcaagccagctctttctccaccagagcacgcacctcaaaatcacttcttgagtctgctagaagaaaaaacagaacctagtctgagactaagttctgtcgctgttataaacttcaaagaaaa Mask Tandem Repeat Region ================================================ ttttctttgaagtttataacagcgacagaacttagtctcagactaggttctgttttttcttctagcagactcaagaagtgattttgaggtgcgtgctctggtggagaaagagctggcttgaagatgcgggtgggaaatgataatgagaagaattttccacagatcttatccccttaaaataaagatgtttcaatttgatgaaattctgtggataacctttattatttcattcaactatgttacaatgttactataaataaaatagaagaggtgt Find is-nt database================================================ Query_seq: SSA_0858:SSA_0859|SSA_0858:SSA_0859:DTDP-L-rhamnose synthase, putative:Triosephosphate isomerase, putative:->->:846507..846780 274 ttttctttgaagtttataacagcgacagaacttagtctcagactaggttctgttttttcttctagcagactcaagaagtgattttgaggtgcgtgctctggtggagaaagagctggcttgaagatgcgggtgggaaatgataatgagaagaattttccacagatcttatccccttaaaataaagatgtttcaatttgatgaaattctgtggataacctttattatttcattcaactatgttacaatgttactataaataaaatagaagaggtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0858:SSA_0859|SSA_0858:SSA_0859:DTDP-L-rhamnose synthase, putative:Triosephosphate isomerase, putative:->->:846507..846780 274 ttttctttgaagtttataacagcgacagaacttagtctcagactaggttctgttttttcttctagcagactcaagaagtgattttgaggtgcgtgctctggtggagaaagagctggcttgaagatgcgggtgggaaatgataatgagaagaattttccacagatcttatccccttaaaataaagatgtttcaatttgatgaaattctgtggataacctttattatttcattcaactatgttacaatgttactataaataaaatagaagaggtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0858:SSA_0859|SSA_0858:SSA_0859:DTDP-L-rhamnose synthase, putative:Triosephosphate isomerase, putative:->->:846507..846780 274 ttttctttgaagtttataacagcgacagaacttagtctcagactaggttctgttttttcttctagcagactcaagaagtgattttgaggtgcgtgctctggtggagaaagagctggcttgaagatgcgggtgggaaatgataatgagaagaattttccacagatcttatccccttaaaataaagatgtttcaatttgatgaaattctgtggataacctttattatttcattcaactatgttacaatgttactataaataaaatagaagaggtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttctttgaagtttataacagcgacagaacttagtctcagactaggttctgttttttcttctagcagactcaagaagtgattttgaggtgcgtgctctggtggagaaagagctggcttgaagatgcgggtgggaaatgataatgagaagaattttccacagatcttatccccttaaaataaagatgtttcaatttgatgaaattctgtggataacctttattatttcattcaactatgttacaatgttactataaataaaatagaagaggtgt Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 137 End: 253 ........................................................................................................................................ M I M R R I F H R S Y P L K I K M F Q F D E I L W I T F I I S F N Y V T M L L ..................... Protein_Len: 42 Strand: - Start: 74 End: 199 ......................................................................... S T I K L H T S Q H L F L Q S S S A P P F H Y H S S N E V S R I G K F Y L H K L K M ........................................................................... Protein_Len: 39 Strand: - Start: 46 End: 162 ............................................. T R N K R R A S E L L S K S T R A R T S F S S A Q L H P H S I I I L L I K W M ................................................................................................................ Protein_Len: 54 Strand: - Start: 3 End: 164 .. E K F N I V A V S S L R L S P E T K E E L L S L F H N Q P A H E P P S L A P K F I R T P F S L S F F K G C M .............................................................................................................. ttttctttgaagtttataacagcgacagaacttagtctcagactaggttctgttttttcttctagcagactcaagaagtgattttgaggtgcgtgctctggtggagaaagagctggcttgaagatgcgggtgggaaatgataatgagaagaattttccacagatcttatccccttaaaataaagatgtttcaatttgatgaaattctgtggataacctttattatttcattcaactatgttacaatgttactataaataaaatagaagaggtgt 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: 82 Start: 217 End: 246 ........................................................................................................................................................................................................................CTTTATTATTTCATTCAACTATGTTACAAT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttctttgaagtttataacagcgacagaacttagtctcagactaggttctgttttttcttctagcagactcaagaagtgattttgaggtgcgtgctctggtggagaaagagctggcttgaagatgcgggtgggaaatgataatgagaagaattttccacagatcttatccccttaaaataaagatgtttcaatttgatgaaattctgtggataacctttattatttcattcaactatgttacaatgttactataaataaaatagaagaggtgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0858:SSA_0859|SSA_0858:SSA_0859:DTDP-L-rhamnose synthase, putative:Triosephosphate isomerase, putative:->->:846507..846780 274 ttttctttgaagtttataacagcgacagaacttagtctcagactaggttctgttttttcttctagcagactcaagaagtgattttgaggtgcgtgctctggtggagaaagagctggcttgaagatgcgggtgggaaatgataatgagaagaattttccacagatcttatccccttaaaataaagatgtttcaatttgatgaaattctgtggataacctttattatttcattcaactatgttacaatgttactataaataaaatagaagaggtgt Intra-Species Hit: Count: 1 Min: 1 Max: 274 Len: 274 Subject: NC_009009_SSA_0858_SSA_0859|DTDP-L-rhamnose synthase, putative:Triosephosphate isomerase, putative|POSITIVE:POSITIVE|[846507,846780]|274 HSP 1 e-value: 1.0E-153 bit: 543.0 Len: 274 Query Start:1 Query End:274 Subject Strand: POSITIVE Subject Start: 1 Subject End: 274 ttttctttgaagtttataacagcgacagaacttagtctcagactaggttctgttttttcttctagcagactcaagaagtgattttgaggtgcgtgctctggtggagaaagagctggcttgaagatgcgggtgggaaatgataatgagaagaattttccacagatcttatccccttaaaataaagatgtttcaatttgatgaaattctgtggataacctttattatttcattcaactatgttacaatgttactataaataaaatagaagaggtgt ttttctttgaagtttataacagcgacagaacttagtctcagactaggttctgttttttcttctagcagactcaagaagtgattttgaggtgcgtgctctggtggagaaagagctggcttgaagatgcgggtgggaaatgataatgagaagaattttccacagatcttatccccttaaaataaagatgtttcaatttgatgaaattctgtggataacctttattatttcattcaactatgttacaatgttactataaataaaatagaagaggtgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUUGAAGUUUAUAACAGCGACAGAACUUAGUCUCAGACUAGGUUCUGUUUUUUCUUCUAGCAGACUCAAGAAGUGAUUUUGAGGUGCGUGCUCUGGUGGAGAAAGAGCUGGCUUGAAGAUGCGGGUGGGAAAUGAUAAUGAGAAGAAUUUUCCACAGAUCUUAUCCCCUUAAAAUAAAGAUGUUUCAAUUUGAUGAAAUUCUGUGGAUAACCUUUAUUAUUUCAUUCAACUAUGUUACAAUGUUACUAUAAAUAAAAUAGAAGAGGUGU ((((((.....(((((((...((.(((((((((((((...)))))))))))))....(((((.(((...(((((((.....)))))))......(((((.........)))))..))).))))).))..((((..(((((.(((((((((.....((((((((..(((((......(((((....)))))......)))))...))))))))....)))).))))))))))...)))).............))))))).....))))))..... (-71.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACACCUCUUCUAUUUUAUUUAUAGUAACAUUGUAACAUAGUUGAAUGAAAUAAUAAAGGUUAUCCACAGAAUUUCAUCAAAUUGAAACAUCUUUAUUUUAAGGGGAUAAGAUCUGUGGAAAAUUCUUCUCAUUAUCAUUUCCCACCCGCAUCUUCAAGCCAGCUCUUUCUCCACCAGAGCACGCACCUCAAAAUCACUUCUUGAGUCUGCUAGAAGAAAAAACAGAACCUAGUCUGAGACUAAGUUCUGUCGCUGUUAUAAACUUCAAAGAAAA .....((((((((.......)))).....(((((((...(..(((((((((.(.((..(((.((((((((.(((.(((...((((((........))))))...))).))))))))))).)))..)).).))).))))))..)....((.(((((......(((((.........)))))..(((.(((((.........)))))..)))..)))))....(((((((.(((((...))))).))))))).)).)))))))......))))... (-61.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 135 92 79 32 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 341 135 91 163 109 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 341 134 92 210 165 NC_009009:SSA_0162|5end_hypothetical_protein_161391..161621_POSITIVE 324 124 87 156 115 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 321 139 98 50 1 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 315 133 91 208 163 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 315 100 56 124 67 NC_009009:SSA_0473|5end_Precorrin-6x_reductase,_putative_475502..475732_POSITIVE 314 127 92 113 70 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 311 130 87 52 8 NC_009009:SSA_1623|5end_50S_ribosomal_protein_L11,_putative_1625968..1626198_NEGATIVE 311 130 81 226 168 NC_009009:SSA_0205|5end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_202722..202952_POSITIVE 309 140 95 81 37 NC_009009:SSA_1746|5end_hypothetical_protein_1732945..1733175_NEGATIVE 308 114 71 170 122 NC_009009:SSA_0107|5end_50S_ribosomal_protein_L3,_putative_108165..108395_POSITIVE 306 149 103 66 23 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 306 133 91 206 158 NC_009009:SSA_0467|5end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_470588..470818_POSITIVE 302 135 91 184 138 NC_009009:SSA_1164|5end_hypothetical_protein_1191138..1191368_NEGATIVE 301 130 87 214 148 NC_009009:SSA_0935|5end_tRNA_pseudouridine_synthase_B,_putative_944015..944245_POSITIVE 300 135 91 225 177 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 298 98 64 169 140 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 297 136 94 227 194 NC_009009:SSA_2263|5end_Ribonucleotide_reductase_(NrdI_family_protein),_putative_2261176..2261406_NEGATIVE 297 69 21 203 155 NC_009009:SSA_2233|5end_hypothetical_protein_2233110..2233340_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 139 92 63 10 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 359 135 92 82 35 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 358 120 79 115 75 NC_009009:SSA_0314|3end_Nucleoside-diphosphate-sugar_epimerase,_putative_308967..309117_NEGATIVE 354 140 91 78 17 NC_009009:SSA_1777|3end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1764427..1764577_NEGATIVE 351 53 11 66 20 NC_009009:SSA_0858|3end_DTDP-L-rhamnose_synthase,_putative_846446..846596_POSITIVE 347 137 95 150 110 NC_009009:SSA_1535|3end_hypothetical_protein_1542457..1542607_NEGATIVE 327 120 71 69 17 NC_009009:SSA_1203|3end_hypothetical_protein_1227628..1227778_POSITIVE 325 121 81 143 100 NC_009009:SSA_0596|3end_hypothetical_protein_587352..587502_POSITIVE 315 100 56 127 70 NC_009009:SSA_0472|3end_Precorrin-3B_C17-methyltransferase,_putative_475585..475735_POSITIVE 309 140 95 88 44 NC_009009:SSA_1747|3end_hypothetical_protein_1732938..1733088_NEGATIVE 309 127 81 120 75 NC_009009:SSA_1480|3end_hypothetical_protein_1483960..1484110_NEGATIVE 308 114 71 85 37 NC_009009:SSA_0106|3end_30S_ribosomal_protein_S10,_putative_108160..108310_POSITIVE 306 149 103 73 30 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 297 69 21 72 24 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 297 67 21 85 41 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 293 134 91 69 16 NC_009009:SSA_0425|3end_Glycosyltransferase,_putative_422230..422380_NEGATIVE 292 127 88 85 43 NC_009009:SSA_1463|3end_Shikimate_kinase,_putative_1469764..1469914_NEGATIVE 292 127 89 107 64 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 290 135 93 36 2 NC_009009:SSA_2168|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+],_putative_2168563..2168713_POSITIVE 290 131 95 131 101 NC_009009:SSA_1476|3end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1482448..1482598_POSITIVE