Origin IGS: gatatcatactgaccttcaatgaaatctagtagagtatttctaactgaatctcactcatttgcccatgaaacatacccaatgaaagctctggaaatcactcctgtaattttgaaaccttctgatcattgtgtcactttatgtaannnnnttaattaattaannnnngtgctggaaagacagcgcaagcgaagccagcggctaaaaaagcgatcgatgacgcgttagttgataagattaaagaaatcgaagcaaataacaacttaacagacgaagaaaaagccgcagctaagcaagaagcgcaagccaaagcagacgcagcgaaacaagcaatcgacaacgcaacaacaaacgatgcagttgagaaagctaaaaacgatgga .........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 tccatcgtttttagctttctcaactgcatcgtttgttgttgcgttgtcgattgcttgtttcgctgcgtctgctttggcttgcgcttcttgcttagctgcggctttttcttcgtctgttaagttgttatttgcttcgatttctttaatcttatcaactaacgcgtcatcgatcgcttttttagccgctggcttcgcttgcgctgtctttccagcacnnnnnttaattaattaannnnnttacataaagtgacacaatgatcagaaggtttcaaaattacaggagtgatttccagagctttcattgggtatgtttcatgggcaaatgagtgagattcagttagaaatactctactagatttcattgaaggtcagtatgatatc Mask Tandem Repeat Region ================================================ gatatcatactgaccttcaatgaaatctagtagagtatttctaactgaatctcactcatttgcccatgaaacatacccaatgaaagctctggaaatcactcctgtaattttgaaaccttctgatcattgtgtcactttatgtaannnnnttaattaattaannnnngtgctggaaagacagcgcaagcgaagccagcggctaaaaaagcgatcgatgacgcgttagttgataagattaaagaaatcgaagcaaataacaacttaacagacgaagaaaaagccgcagctaagcaagaagcgcaagccaaagcagacgcagcgaaacaagcaatcgacaacgcaacaacaaacgatgcagttgagaaagctaaaaacgatgga Find is-nt database================================================ Query_seq: SMT_1969:SMT_1970|SMT_1969:SMT_1970:transcription-repair coupling factor:hypothetical protein predicted by Glimmer/Critica:<-->:1901782..1902162 381 gatatcatactgaccttcaatgaaatctagtagagtatttctaactgaatctcactcatttgcccatgaaacatacccaatgaaagctctggaaatcactcctgtaattttgaaaccttctgatcattgtgtcactttatgtaannnnnttaattaattaannnnngtgctggaaagacagcgcaagcgaagccagcggctaaaaaagcgatcgatgacgcgttagttgataagattaaagaaatcgaagcaaataacaacttaacagacgaagaaaaagccgcagctaagcaagaagcgcaagccaaagcagacgcagcgaaacaagcaatcgacaacgcaacaacaaacgatgcagttgagaaagctaaaaacgatgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1969:SMT_1970|SMT_1969:SMT_1970:transcription-repair coupling factor:hypothetical protein predicted by Glimmer/Critica:<-->:1901782..1902162 381 gatatcatactgaccttcaatgaaatctagtagagtatttctaactgaatctcactcatttgcccatgaaacatacccaatgaaagctctggaaatcactcctgtaattttgaaaccttctgatcattgtgtcactttatgtaannnnnttaattaattaannnnngtgctggaaagacagcgcaagcgaagccagcggctaaaaaagcgatcgatgacgcgttagttgataagattaaagaaatcgaagcaaataacaacttaacagacgaagaaaaagccgcagctaagcaagaagcgcaagccaaagcagacgcagcgaaacaagcaatcgacaacgcaacaacaaacgatgcagttgagaaagctaaaaacgatgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1969:SMT_1970|SMT_1969:SMT_1970:transcription-repair coupling factor:hypothetical protein predicted by Glimmer/Critica:<-->:1901782..1902162 381 gatatcatactgaccttcaatgaaatctagtagagtatttctaactgaatctcactcatttgcccatgaaacatacccaatgaaagctctggaaatcactcctgtaattttgaaaccttctgatcattgtgtcactttatgtaannnnnttaattaattaannnnngtgctggaaagacagcgcaagcgaagccagcggctaaaaaagcgatcgatgacgcgttagttgataagattaaagaaatcgaagcaaataacaacttaacagacgaagaaaaagccgcagctaagcaagaagcgcaagccaaagcagacgcagcgaaacaagcaatcgacaacgcaacaacaaacgatgcagttgagaaagctaaaaacgatgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatatcatactgaccttcaatgaaatctagtagagtatttctaactgaatctcactcatttgcccatgaaacatacccaatgaaagctctggaaatcactcctgtaattttgaaaccttctgatcattgtgtcactttatgtaannnnnttaattaattaannnnngtgctggaaagacagcgcaagcgaagccagcggctaaaaaagcgatcgatgacgcgttagttgataagattaaagaaatcgaagcaaataacaacttaacagacgaagaaaaagccgcagctaagcaagaagcgcaagccaaagcagacgcagcgaaacaagcaatcgacaacgcaacaacaaacgatgcagttgagaaagctaaaaacgatgga Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 20 End: 154 ................... M K S S R V F L T E S H S F A H E T Y P M K A L E I T P V I L K P S D H C V T L C X X X N ................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 157 End: 381 ............................................................................................................................................................ M X X X A G K T A Q A K P A A K K A I D D A L V D K I K E I E A N N N L T D E E K A A A K Q E A Q A K A D A A K Q A I D Protein_Len: 38 Strand: - Start: 265 End: 378 ........................................................................................................................................................................................................................................................................ C V F F F G C S L L F R L G F C V C R F L C D V V C C C V I C N L F S F V M ... Protein_Len: 60 Strand: - Start: 153 End: 338 ........................................................................................................................................................ L X X A P F V A C A F G A A L F A I S S A N T S L I L S I S A F L L K V S S S F A A A L C S A C A L A S A A F C A I S M ........................................... gatatcatactgaccttcaatgaaatctagtagagtatttctaactgaatctcactcatttgcccatgaaacatacccaatgaaagctctggaaatcactcctgtaattttgaaaccttctgatcattgtgtcactttatgtaannnnnttaattaattaannnnngtgctggaaagacagcgcaagcgaagccagcggctaaaaaagcgatcgatgacgcgttagttgataagattaaagaaatcgaagcaaataacaacttaacagacgaagaaaaagccgcagctaagcaagaagcgcaagccaaagcagacgcagcgaaacaagcaatcgacaacgcaacaacaaacgatgcagttgagaaagctaaaaacgatgga Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatatcatactgaccttcaatgaaatctagtagagtatttctaactgaatctcactcatttgcccatgaaacatacccaatgaaagctctggaaatcactcctgtaattttgaaaccttctgatcattgtgtcactttatgtaannnnnttaattaattaannnnngtgctggaaagacagcgcaagcgaagccagcggctaaaaaagcgatcgatgacgcgttagttgataagattaaagaaatcgaagcaaataacaacttaacagacgaagaaaaagccgcagctaagcaagaagcgcaagccaaagcagacgcagcgaaacaagcaatcgacaacgcaacaacaaacgatgcagttgagaaagctaaaaacgatgga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -3.1 Tail_Score: -5.02074 Start: 208 End: 221 Full_Region: atcttatcaactaac gcgtc atc gatcgc ttttttagccgctgg ...............................................................................................................................................................................................................gcgtcatcgatcgc................................................................................................................................................................ Find igs database================================================ Query_seq: SMT_1969:SMT_1970|SMT_1969:SMT_1970:transcription-repair coupling factor:hypothetical protein predicted by Glimmer/Critica:<-->:1901782..1902162 381 gatatcatactgaccttcaatgaaatctagtagagtatttctaactgaatctcactcatttgcccatgaaacatacccaatgaaagctctggaaatcactcctgtaattttgaaaccttctgatcattgtgtcactttatgtaannnnnttaattaattaannnnngtgctggaaagacagcgcaagcgaagccagcggctaaaaaagcgatcgatgacgcgttagttgataagattaaagaaatcgaagcaaataacaacttaacagacgaagaaaaagccgcagctaagcaagaagcgcaagccaaagcagacgcagcgaaacaagcaatcgacaacgcaacaacaaacgatgcagttgagaaagctaaaaacgatgga Intra-Species Hit: Count: 1 Min: 1 Max: 381 Len: 381 Subject: smit_SMT_1969_SMT_1970|transcription-repair coupling factor:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:POSITIVE|[1901782,1902162]|381 HSP 1 e-value: 0.0 bit: 696.0 Len: 381 Query Start:1 Query End:381 Subject Strand: POSITIVE Subject Start: 1 Subject End: 381 gatatcatactgaccttcaatgaaatctagtagagtatttctaactgaatctcactcatttgcccatgaaacatacccaatgaaagctctggaaatcactcctgtaattttgaaaccttctgatcattgtgtcactttatgtaannnnnttaattaattaannnnngtgctggaaagacagcgcaagcgaagccagcggctaaaaaagcgatcgatgacgcgttagttgataagattaaagaaatcgaagcaaataacaacttaacagacgaagaaaaagccgcagctaagcaagaagcgcaagccaaagcagacgcagcgaaacaagcaatcgacaacgcaacaacaaacgatgcagttgagaaagctaaaaacgatgga gatatcatactgaccttcaatgaaatctagtagagtatttctaactgaatctcactcatttgcccatgaaacatacccaatgaaagctctggaaatcactcctgtaattttgaaaccttctgatcattgtgtcactttatgtaannnnnttaattaattaannnnngtgctggaaagacagcgcaagcgaagccagcggctaaaaaagcgatcgatgacgcgttagttgataagattaaagaaatcgaagcaaataacaacttaacagacgaagaaaaagccgcagctaagcaagaagcgcaagccaaagcagacgcagcgaaacaagcaatcgacaacgcaacaacaaacgatgcagttgagaaagctaaaaacgatgga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUCAUACUGACCUUCAAUGAAAUCUAGUAGAGUAUUUCUAACUGAAUCUCACUCAUUUGCCCAUGAAACAUACCCAAUGAAAGCUCUGGAAAUCACUCCUGUAAUUUUGAAACCUUCUGAUCAUUGUGUCACUUUAUGUAANNNNNUUAAUUAAUUAANNNNNGUGCUGGAAAGACAGCGCAAGCGAAGCCAGCGGCUAAAAAAGCGAUCGAUGACGCGUUAGUUGAUAAGAUUAAAGAAAUCGAAGCAAAUAACAACUUAACAGACGAAGAAAAAGCCGCAGCUAAGCAAGAAGCGCAAGCCAAAGCAGACGCAGCGAAACAAGCAAUCGACAACGCAACAACAAACGAUGCAGUUGAGAAAGCUAAAAACGAUGGA (((.((((..((.....)))))).))).....(((((((((((............((((......))))..(((.....))).......))))))).))))..............((.((...((.(((((((.((((............................((((((......))))))..((..(((..((((((......((..(((((..(...((((((.....)))))).)..))))).)).........(((........)))....)))))).)))..)).....((....)).))))..))))))).))....(((..((..(((((((.(.......).))).)))).))..)))......)).)). (-77.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCAUCGUUUUUAGCUUUCUCAACUGCAUCGUUUGUUGUUGCGUUGUCGAUUGCUUGUUUCGCUGCGUCUGCUUUGGCUUGCGCUUCUUGCUUAGCUGCGGCUUUUUCUUCGUCUGUUAAGUUGUUAUUUGCUUCGAUUUCUUUAAUCUUAUCAACUAACGCGUCAUCGAUCGCUUUUUUAGCCGCUGGCUUCGCUUGCGCUGUCUUUCCAGCACNNNNNUUAAUUAAUUAANNNNNUUACAUAAAGUGACACAAUGAUCAGAAGGUUUCAAAAUUACAGGAGUGAUUUCCAGAGCUUUCAUUGGGUAUGUUUCAUGGGCAAAUGAGUGAGAUUCAGUUAGAAAUACUCUACUAGAUUUCAUUGAAGGUCAGUAUGAUAUC ......((((((((((.(((((......((((((((((..((((....(((((.((((.(((((((((..((....))..)))).....((..((((((((((.......((((.((...((.((((.(((.(..((((.....))))..).))).))))))...)).)).)).......)))))).))))..))....((((......))))................................))))).))))))))).((((((((..(((((((....)))))))...)))))))).......))))..))...)))))))).)))))...))))))))))..((((((.(((((......))))))))).)).... (-89.24) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 898 100 51 191 142 smit:SMT_1969|5end_transcription-repair_coupling_factor_1901691..1901921_NEGATIVE 392 330 281 71 18 smit:SMT_147|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_97406..97636_POSITIVE 392 330 281 71 18 smit:SMT_119|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_70457..70687_POSITIVE 355 329 281 74 21 smit:SMT_151|5end_K02073_D-methionine_transport_system_substrate-binding_protein_99474..99704_POSITIVE 344 329 281 77 21 smit:SMT_274|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_215221..215451_POSITIVE 338 223 181 142 106 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 335 329 281 218 174 smit:SMT_1982|5end_conserved_hypothetical_protein_1913036..1913266_POSITIVE 335 329 281 206 162 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 335 329 281 231 187 smit:SMT_1156|5end_K07485_transposase_1099938..1100168_POSITIVE 335 321 281 68 15 smit:SMT_1142|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1085546..1085776_POSITIVE 321 310 261 75 33 smit:SMT_935|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_887326..887556_POSITIVE 319 225 184 179 139 smit:SMT_857|5end_endo-beta-N-acetylglucosaminidase_802491..802721_NEGATIVE 315 320 281 166 127 smit:SMT_2067|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1973432..1973662_POSITIVE 315 210 169 200 152 smit:SMT_1972|5end_uncharacterized_conserved_phage_related_protein_1903662..1903892_POSITIVE 315 210 169 178 130 smit:SMT_325|5end_K02029_polar_amino_acid_transport_system_permease_protein_263023..263253_NEGATIVE 312 220 175 227 178 smit:SMT_1739|5end_hypothetical_protein_1721263..1721493_POSITIVE 312 221 183 58 24 smit:SMT_1382|5end_glutamate_5-kinase_1360744..1360974_NEGATIVE 306 209 170 51 13 smit:SMT_807|5end_hypothetical_protein_predicted_by_Glimmer/Critica_716815..717045_NEGATIVE 305 326 281 72 21 smit:SMT_1293|5end_K02051_sulfonate/nitrate/taurine_transport_system_substrate-binding_protein_1254976..1255206_POSITIVE 300 320 276 56 17 smit:SMT_854|5end_hypothetical_protein_799492..799722_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 466 370 328 47 5 smit:SMT_2092|3end_malolactic_enzyme_1987040..1987190_NEGATIVE 457 228 182 77 32 smit:SMT_2057|3end_cell_division_protein_FtsH_1966897..1967047_NEGATIVE 319 225 184 145 105 smit:SMT_858|3end_triosephosphate_isomerase_802525..802675_NEGATIVE 316 201 167 148 115 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 300 320 276 56 17 smit:SMT_855|3end_dihydrofolate_reductase_799492..799642_NEGATIVE 287 217 171 74 28 smit:SMT_794|3end_hypothetical_protein_703245..703395_NEGATIVE 285 320 280 60 12 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 281 200 151 101 52 smit:SMT_227|3end_hypothetical_protein_164418..164568_POSITIVE 279 226 181 75 15 smit:SMT_2073|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1977074..1977224_POSITIVE 276 199 151 143 92 smit:SMT_2028|3end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1943367..1943517_NEGATIVE 276 320 280 150 111 smit:SMT_1646|3end_3-isopropylmalate_dehydratase_large_subunit_1633473..1633623_POSITIVE 275 200 168 36 4 smit:SMT_1639|3end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1624803..1624953_NEGATIVE 275 199 167 58 28 smit:SMT_173|3end_50S_ribosomal_protein_L2_117407..117557_POSITIVE 271 321 282 148 101 smit:SMT_807|3end_hypothetical_protein_predicted_by_Glimmer/Critica_716708..716858_NEGATIVE 269 182 150 126 91 smit:SMT_2040|3end_transcription-repair_coupling_factor_1950463..1950613_NEGATIVE 269 209 167 148 104 smit:SMT_1885|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1839830..1839980_NEGATIVE 269 78 31 75 28 smit:SMT_234|3end_aminopeptidase_PepS_174151..174301_POSITIVE 265 204 170 56 27 smit:SMT_1491|3end_capsular_polysaccharide_biosynthesis_protein,_putative_1471967..1472117_POSITIVE 265 209 169 79 31 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 265 305 261 83 42 smit:SMT_441|3end_L-lactate_oxidase_381279..381429_POSITIVE