Origin IGS: tgcagaaacgagcaagatgaacattttgcttaagatcatgcagacaatagggtgggacaaaatgacatttgtctcaccttttttgaataaaaagattgaggtttatttcacagaccgttaaaatagaaagtctttataagaacacaatatttgttcctaaggttattaagattactatccgtgagattactcttcatattatgaagagtaatgtgcttgtctccgttccaataaagttcttgttttctgattttgagcaaaatagttttgttcgtcaaagaattcatatataatatacggtacaaagagaggacgagt .........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 actcgtcctctctttgtaccgtatattatatatgaattctttgacgaacaaaactattttgctcaaaatcagaaaacaagaactttattggaacggagacaagcacattactcttcataatatgaagagtaatctcacggatagtaatcttaataaccttaggaacaaatattgtgttcttataaagactttctattttaacggtctgtgaaataaacctcaatctttttattcaaaaaaggtgagacaaatgtcattttgtcccaccctattgtctgcatgatcttaagcaaaatgttcatcttgctcgtttctgca Mask Tandem Repeat Region ================================================ tgcagaaacgagcaagatgaacattttgcttaagatcatgcagacaatagggtgggacaaaatgacatttgtctcaccttttttgaataaaaagattgaggtttatttcacagaccgttaaaatagaaagtctttataagaacacaatatttgttcctaaggttattaagattactatccgtgagattactcttcatattatgaagagtaatgtgcttgtctccgttccaataaagttcttgttttctgattttgagcaaaatagttttgttcgtcaaagaattcatatataatatacggtacaaagagaggacgagt Find is-nt database================================================ Query_seq: SSA_0182:SSA_0183|SSA_0182:SSA_0183:Endoglucanase, putative:hypothetical protein:->->:187468..187785 318 tgcagaaacgagcaagatgaacattttgcttaagatcatgcagacaatagggtgggacaaaatgacatttgtctcaccttttttgaataaaaagattgaggtttatttcacagaccgttaaaatagaaagtctttataagaacacaatatttgttcctaaggttattaagattactatccgtgagattactcttcatattatgaagagtaatgtgcttgtctccgttccaataaagttcttgttttctgattttgagcaaaatagttttgttcgtcaaagaattcatatataatatacggtacaaagagaggacgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0182:SSA_0183|SSA_0182:SSA_0183:Endoglucanase, putative:hypothetical protein:->->:187468..187785 318 tgcagaaacgagcaagatgaacattttgcttaagatcatgcagacaatagggtgggacaaaatgacatttgtctcaccttttttgaataaaaagattgaggtttatttcacagaccgttaaaatagaaagtctttataagaacacaatatttgttcctaaggttattaagattactatccgtgagattactcttcatattatgaagagtaatgtgcttgtctccgttccaataaagttcttgttttctgattttgagcaaaatagttttgttcgtcaaagaattcatatataatatacggtacaaagagaggacgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0182:SSA_0183|SSA_0182:SSA_0183:Endoglucanase, putative:hypothetical protein:->->:187468..187785 318 tgcagaaacgagcaagatgaacattttgcttaagatcatgcagacaatagggtgggacaaaatgacatttgtctcaccttttttgaataaaaagattgaggtttatttcacagaccgttaaaatagaaagtctttataagaacacaatatttgttcctaaggttattaagattactatccgtgagattactcttcatattatgaagagtaatgtgcttgtctccgttccaataaagttcttgttttctgattttgagcaaaatagttttgttcgtcaaagaattcatatataatatacggtacaaagagaggacgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcagaaacgagcaagatgaacattttgcttaagatcatgcagacaatagggtgggacaaaatgacatttgtctcaccttttttgaataaaaagattgaggtttatttcacagaccgttaaaatagaaagtctttataagaacacaatatttgttcctaaggttattaagattactatccgtgagattactcttcatattatgaagagtaatgtgcttgtctccgttccaataaagttcttgttttctgattttgagcaaaatagttttgttcgtcaaagaattcatatataatatacggtacaaagagaggacgagt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 17 End: 118 ................ M N I L L K I M Q T I G W D K M T F V S P F L N K K I E V Y F T D R ........................................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 87 End: 290 ...................................................................................... M K R L R F I S Q T V K I E S L Y K N T I F V P K V I K I T I R E I T L H I M K S N V L V S V P I K F L F S D F E Q N S ............................ Protein_Len: 31 Strand: - Start: 202 End: 294 ......................................................................................................................................................................................................... S S Y H A Q R R E L L T R T K Q N Q A F Y N Q E D F F E Y I M ........................ Protein_Len: 60 Strand: - Start: 111 End: 305 .............................................................................................................. F T K I L V C Y K N R L N N L N S D T L N S K M N H L T I H K D G N W Y L E Q K R I K L L I T K N T L S N M Y L I R Y M ............. Protein_Len: 32 Strand: - Start: 1 End: 96 A S V L L I F M K S L I M C V I P H S L I V N T E G K K F L F M .............................................................................................................................................................................................................................. tgcagaaacgagcaagatgaacattttgcttaagatcatgcagacaatagggtgggacaaaatgacatttgtctcaccttttttgaataaaaagattgaggtttatttcacagaccgttaaaatagaaagtctttataagaacacaatatttgttcctaaggttattaagattactatccgtgagattactcttcatattatgaagagtaatgtgcttgtctccgttccaataaagttcttgttttctgattttgagcaaaatagttttgttcgtcaaagaattcatatataatatacggtacaaagagaggacgagt 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: 85 Start: 95 End: 124 ..............................................................................................ATTGAGGTTTATTTCACAGACCGTTAAAAT.................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 250 End: 279 .........................................................................................................................................................................................................................................................TTTGACGAACAAAACTATTTTGCTCAAAAT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgcagaaacgagcaagatgaacattttgcttaagatcatgcagacaatagggtgggacaaaatgacatttgtctcaccttttttgaataaaaagattgaggtttatttcacagaccgttaaaatagaaagtctttataagaacacaatatttgttcctaaggttattaagattactatccgtgagattactcttcatattatgaagagtaatgtgcttgtctccgttccaataaagttcttgttttctgattttgagcaaaatagttttgttcgtcaaagaattcatatataatatacggtacaaagagaggacgagt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -2.4 Tail_Score: -3.53164 Start: 48 End: 81 Full_Region: atctttttattcaaa aaaggtgagacaaa tgtcat tttgtcccacccta ttgtctgcatgatct ...............................................aaaggtgagacaaatgtcattttgtcccacccta............................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 54 HP_score: -5.0 Tail_Score: -3.33792 Start: 50 End: 79 Full_Region: ctttttattcaaaaa aggtgagacaaa tgtcat tttgtcccaccc tattgtctgcatgat .................................................aggtgagacaaatgtcattttgtcccaccc............................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -10.7 Tail_Score: -5.08824 Start: 51 End: 78 Full_Region: TCATGCAGACAATAG GGTGGGACAAA ATGACA TTTGTCTCACC TTTTTTGAATAAAAA ..................................................GGTGGGACAAAATGACATTTGTCTCACC................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 69 HP_score: -8.5 Tail_Score: -2.59793 Start: 51 End: 78 Full_Region: tttttattcaaaaaa ggtgagacaaa tgtcat tttgtcccacc ctattgtctgcatga ..................................................ggtgagacaaatgtcattttgtcccacc................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 71 HP_score: -7.7 Tail_Score: -3.551 Start: 183 End: 216 Full_Region: AAGATTACTATCCGT GAGATTACTCTTCAT ATT ATGAAGAGTAATGTGC TTGTCTCCGTTCCAA ......................................................................................................................................................................................GAGATTACTCTTCATATTATGAAGAGTAATGTGC...................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -13.1 Tail_Score: -2.99717 Start: 187 End: 211 Full_Region: TTACTATCCGTGAGA TTACTCTTCAT ATT ATGAAGAGTAA TGTGCTTGTCTCCGT ..........................................................................................................................................................................................TTACTCTTCATATTATGAAGAGTAA........................................................................................................... TransTerm Strand: - Conf: 80 HP_score: -10.4 Tail_Score: -2.62616 Start: 190 End: 208 Full_Region: gagacaagcacatta ctcttcat aat atgaagag taatctcacggatag .............................................................................................................................................................................................ctcttcataatatgaagag.............................................................................................................. Find igs database================================================ Query_seq: SSA_0182:SSA_0183|SSA_0182:SSA_0183:Endoglucanase, putative:hypothetical protein:->->:187468..187785 318 tgcagaaacgagcaagatgaacattttgcttaagatcatgcagacaatagggtgggacaaaatgacatttgtctcaccttttttgaataaaaagattgaggtttatttcacagaccgttaaaatagaaagtctttataagaacacaatatttgttcctaaggttattaagattactatccgtgagattactcttcatattatgaagagtaatgtgcttgtctccgttccaataaagttcttgttttctgattttgagcaaaatagttttgttcgtcaaagaattcatatataatatacggtacaaagagaggacgagt Intra-Species Hit: Count: 1 Min: 1 Max: 318 Len: 318 Subject: NC_009009_SSA_0182_SSA_0183|Endoglucanase, putative:hypothetical protein|POSITIVE:POSITIVE|[187468,187785]|318 HSP 1 e-value: 1.0E-180 bit: 630.0 Len: 318 Query Start:1 Query End:318 Subject Strand: POSITIVE Subject Start: 1 Subject End: 318 tgcagaaacgagcaagatgaacattttgcttaagatcatgcagacaatagggtgggacaaaatgacatttgtctcaccttttttgaataaaaagattgaggtttatttcacagaccgttaaaatagaaagtctttataagaacacaatatttgttcctaaggttattaagattactatccgtgagattactcttcatattatgaagagtaatgtgcttgtctccgttccaataaagttcttgttttctgattttgagcaaaatagttttgttcgtcaaagaattcatatataatatacggtacaaagagaggacgagt tgcagaaacgagcaagatgaacattttgcttaagatcatgcagacaatagggtgggacaaaatgacatttgtctcaccttttttgaataaaaagattgaggtttatttcacagaccgttaaaatagaaagtctttataagaacacaatatttgttcctaaggttattaagattactatccgtgagattactcttcatattatgaagagtaatgtgcttgtctccgttccaataaagttcttgttttctgattttgagcaaaatagttttgttcgtcaaagaattcatatataatatacggtacaaagagaggacgagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAGAAACGAGCAAGAUGAACAUUUUGCUUAAGAUCAUGCAGACAAUAGGGUGGGACAAAAUGACAUUUGUCUCACCUUUUUUGAAUAAAAAGAUUGAGGUUUAUUUCACAGACCGUUAAAAUAGAAAGUCUUUAUAAGAACACAAUAUUUGUUCCUAAGGUUAUUAAGAUUACUAUCCGUGAGAUUACUCUUCAUAUUAUGAAGAGUAAUGUGCUUGUCUCCGUUCCAAUAAAGUUCUUGUUUUCUGAUUUUGAGCAAAAUAGUUUUGUUCGUCAAAGAAUUCAUAUAUAAUAUACGGUACAAAGAGAGGACGAGU .......(((((((((((....((((((((((((((((.(.(((((..(((((((((((((......))))))))))))).................(((.((((((..((((((.......((((..((((((.(((((((((.......)))))......)))).)))))).))))..((.(.((((((((((((...)))))))))))).)))..))))..))...)))))).))).))))).))))))))))))))))).)))))))))))........................................... (-79.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCGUCCUCUCUUUGUACCGUAUAUUAUAUAUGAAUUCUUUGACGAACAAAACUAUUUUGCUCAAAAUCAGAAAACAAGAACUUUAUUGGAACGGAGACAAGCACAUUACUCUUCAUAAUAUGAAGAGUAAUCUCACGGAUAGUAAUCUUAAUAACCUUAGGAACAAAUAUUGUGUUCUUAUAAAGACUUUCUAUUUUAACGGUCUGUGAAAUAAACCUCAAUCUUUUUAUUCAAAAAAGGUGAGACAAAUGUCAUUUUGUCCCACCCUAUUGUCUGCAUGAUCUUAAGCAAAAUGUUCAUCUUGCUCGUUUCUGCA ..............((((.((((((...))))))........(((((.((((((.((((((((.((.((((.....(((........)))....(.((((((....((((((((((((...)))))))))))).((((((((.((..............((((((((.......))))))))...((.....))......)).)))))))).............................((((.((((((......)))))).))))...)))))).).)))).)).)))))))))))....))).)))))..)))) (-69.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 58 12 217 179 NC_009009:SSA_1779|5end_Segregation_and_condensation_protein_A,_putative_1766414..1766644_NEGATIVE 302 259 215 196 152 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 282 50 1 78 21 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 277 76 38 161 119 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 276 59 11 210 162 NC_009009:SSA_0307|5end_Glutamine_synthetase_type_1,_putative_302987..303217_POSITIVE 265 250 201 214 163 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 263 74 34 220 181 NC_009009:SSA_2011|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012856..2013086_NEGATIVE 262 276 233 223 187 NC_009009:SSA_1704|5end_Conserved_uncharacterized_protein_1696401..1696631_NEGATIVE 262 260 211 182 113 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 260 229 181 96 40 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 255 53 13 67 23 NC_009009:SSA_1474|5end_Lipoprotein,_putative_1479741..1479971_NEGATIVE 254 230 183 103 48 NC_009009:SSA_0774|5end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase,_putative_754571..754801_POSITIVE 252 60 11 93 35 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 250 228 190 93 47 NC_009009:SSA_2018|5end_hypothetical_protein_2018801..2019031_NEGATIVE 250 258 214 82 29 NC_009009:SSA_1153|5end_HemK_protein,_putative_1181838..1182068_POSITIVE 249 89 41 231 175 NC_009009:SSA_1945|5end_Oligopeptide_transport_ATP-binding_protein,_putative_1937689..1937919_NEGATIVE 249 254 213 115 65 NC_009009:SSA_1710|5end_Transcriptional_regulator,_XRE_family,_putative_1698338..1698568_POSITIVE 248 59 12 217 174 NC_009009:SSA_2158|5end_Methyltransferase,_putative_2159053..2159283_NEGATIVE 248 70 23 69 15 NC_009009:SSA_1940|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1927129..1927359_NEGATIVE 248 256 215 94 39 NC_009009:SSA_0554|5end_hypothetical_protein_549265..549495_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 80 49 42 11 NC_009009:SSA_0182|3end_Endoglucanase,_putative_187407..187557_POSITIVE 277 76 38 135 93 NC_009009:SSA_1856|3end_hypothetical_protein_1852077..1852227_NEGATIVE 275 57 11 84 35 NC_009009:SSA_1691|3end_Transcriptional_regulator,_XRE_family,_putative_1683570..1683720_POSITIVE 250 228 190 82 36 NC_009009:SSA_2019|3end_hypothetical_protein_2018812..2018962_NEGATIVE 250 62 21 89 35 NC_009009:SSA_1683|3end_NrdI_protein,_putative_1677034..1677184_NEGATIVE 250 258 214 82 29 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 248 70 23 69 15 NC_009009:SSA_1941|3end_hypothetical_protein_1927129..1927279_NEGATIVE 248 256 215 90 35 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 247 220 172 129 69 NC_009009:SSA_1509|3end_Polysaccharide_biosynthesis_protein/_rhamnosyltransferase,_putative_1513256..1513406_NEGATIVE 246 270 224 131 77 NC_009009:SSA_1335|3end_Ankyrin_repeat_protein,_putative_1349055..1349205_NEGATIVE 245 50 1 61 4 NC_009009:SSA_1794|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1776345..1776495_NEGATIVE 245 56 11 122 62 NC_009009:SSA_0170|3end_hypothetical_protein_168130..168280_NEGATIVE 243 301 262 101 64 NC_009009:SSA_1011|3end_hypothetical_protein_1014804..1014954_POSITIVE 242 256 214 57 7 NC_009009:SSA_0522|3end_Ethanolamine_utilization_protein,_putative_521710..521860_POSITIVE 241 250 207 149 97 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 241 56 23 147 103 NC_009009:SSA_0405|3end_Transcriptional_regulator,_XRE_family,_putative_402115..402265_POSITIVE 236 246 205 148 93 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 232 58 11 62 22 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 232 259 211 146 96 NC_009009:SSA_0285|3end_Formate_acetyltransferase_3,_putative_278879..279029_POSITIVE 231 257 217 49 3 NC_009009:SSA_2268|3end_Type_II_secretory_pathway,_pullulanase_PulA_glycosidase,_putative_2269386..2269536_POSITIVE