Origin IGS: agatttacatgaaaattatagaaaggaacaaaggtgttcagggaattgaacacgggttcccaaatttattactcaatataaaagaaaggaattgaacccgacctaaattctcggaaaaaagataaatctgcctaggagcatcgctccagcgtcagatttcctatttttcagtcgaattttacggtcttggtatcttgt .........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 acaagataccaagaccgtaaaattcgactgaaaaataggaaatctgacgctggagcgatgctcctaggcagatttatcttttttccgagaatttaggtcgggttcaattcctttcttttatattgagtaataaatttgggaacccgtgttcaattccctgaacacctttgttcctttctataattttcatgtaaatct Mask Tandem Repeat Region ================================================ agatttacatgaaaattatagaaaggaacaaaggtgttcagggaattgaacacgggttcccaaatttattactcaatataaaagaaaggaattgaacccgacctaaattctcggaaaaaagataaatctgcctaggagcatcgctccagcgtcagatttcctatttttcagtcgaattttacggtcttggtatcttgt Find is-nt database================================================ Query_seq: SMT_341:SMT_342|SMT_341:SMT_342:ThiJ/PfpI family protein:chaperone protein DnaJ:->->:281742..281939 198 agatttacatgaaaattatagaaaggaacaaaggtgttcagggaattgaacacgggttcccaaatttattactcaatataaaagaaaggaattgaacccgacctaaattctcggaaaaaagataaatctgcctaggagcatcgctccagcgtcagatttcctatttttcagtcgaattttacggtcttggtatcttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_341:SMT_342|SMT_341:SMT_342:ThiJ/PfpI family protein:chaperone protein DnaJ:->->:281742..281939 198 agatttacatgaaaattatagaaaggaacaaaggtgttcagggaattgaacacgggttcccaaatttattactcaatataaaagaaaggaattgaacccgacctaaattctcggaaaaaagataaatctgcctaggagcatcgctccagcgtcagatttcctatttttcagtcgaattttacggtcttggtatcttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_341:SMT_342|SMT_341:SMT_342:ThiJ/PfpI family protein:chaperone protein DnaJ:->->:281742..281939 198 agatttacatgaaaattatagaaaggaacaaaggtgttcagggaattgaacacgggttcccaaatttattactcaatataaaagaaaggaattgaacccgacctaaattctcggaaaaaagataaatctgcctaggagcatcgctccagcgtcagatttcctatttttcagtcgaattttacggtcttggtatcttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agatttacatgaaaattatagaaaggaacaaaggtgttcagggaattgaacacgggttcccaaatttattactcaatataaaagaaaggaattgaacccgacctaaattctcggaaaaaagataaatctgcctaggagcatcgctccagcgtcagatttcctatttttcagtcgaattttacggtcttggtatcttgt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 3 End: 92 .. M Y M K I I E R N K G V Q G I E H G F P N L L L N I K E R N .......................................................................................................... Protein_Len: 30 Strand: + Start: 107 End: 196 .......................................................................................................... M L G K K I N L P R S I A P A S D F L F F S R I L R S W Y L .. agatttacatgaaaattatagaaaggaacaaaggtgttcagggaattgaacacgggttcccaaatttattactcaatataaaagaaaggaattgaacccgacctaaattctcggaaaaaagataaatctgcctaggagcatcgctccagcgtcagatttcctatttttcagtcgaattttacggtcttggtatcttgt 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================================================ agatttacatgaaaattatagaaaggaacaaaggtgttcagggaattgaacacgggttcccaaatttattactcaatataaaagaaaggaattgaacccgacctaaattctcggaaaaaagataaatctgcctaggagcatcgctccagcgtcagatttcctatttttcagtcgaattttacggtcttggtatcttgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_341:SMT_342|SMT_341:SMT_342:ThiJ/PfpI family protein:chaperone protein DnaJ:->->:281742..281939 198 agatttacatgaaaattatagaaaggaacaaaggtgttcagggaattgaacacgggttcccaaatttattactcaatataaaagaaaggaattgaacccgacctaaattctcggaaaaaagataaatctgcctaggagcatcgctccagcgtcagatttcctatttttcagtcgaattttacggtcttggtatcttgt Intra-Species Hit: Count: 1 Min: 1 Max: 198 Len: 198 Subject: smit_SMT_341_SMT_342|ThiJ/PfpI family protein:chaperone protein DnaJ|POSITIVE:POSITIVE|[281742,281939]|198 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 198 Query Start:1 Query End:198 Subject Strand: POSITIVE Subject Start: 1 Subject End: 198 agatttacatgaaaattatagaaaggaacaaaggtgttcagggaattgaacacgggttcccaaatttattactcaatataaaagaaaggaattgaacccgacctaaattctcggaaaaaagataaatctgcctaggagcatcgctccagcgtcagatttcctatttttcagtcgaattttacggtcttggtatcttgt agatttacatgaaaattatagaaaggaacaaaggtgttcagggaattgaacacgggttcccaaatttattactcaatataaaagaaaggaattgaacccgacctaaattctcggaaaaaagataaatctgcctaggagcatcgctccagcgtcagatttcctatttttcagtcgaattttacggtcttggtatcttgt Inter-species Hit: Count: 1 Min: 47 Max: 196 Len: 150 Subject: NC_009009_SSA_2005_SSA_2006|Chaperone protein dnaJ, putative:4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme, putative|NEGATIVE:NEGATIVE|[2006475,2006672]|198 HSP 1 e-value: 8.0E-49 bit: 194.0 Len: 150 Query Start:47 Query End:196 Subject Strand: NEGATIVE Subject Start: 3 Subject End: 152 ..............................................tgaacacgggttcccaaatttattactcaatataaaagaaaggaattgaacccgacctaaattctcggaaaaaagataaatctgcctaggagcatcgctccagcgtcagatttcctatttttcagtcgaattttacggtcttggtatctt.. ..............................................tgaacacgggttccaaaaattctgactcaatataaaagaaaggaactgaacccgacctaaattctcggaaaagagagaaatctgtctaggggcatcgctccgtcgcctgatttcctatttttcagtcgaattttacggtcttggtatctt.. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAACACGGGUUCCCAAAUUUAUUACUCAAUAUAAAAGAAAGGAAUUGAACCCGACCUAAAUUCUCGGAAAAAAGAUAAAUCUGCCUAGGAGCAUCGCUCCAGCGUCAGAUUUCCUAUUUUUCAGUCGAAUUUUACGGUCUUGGUAUCUU .......((((((((...(((((........))))).....))....))))))((((.((((((...((((((....((((((((((.(((((...))))))).).)))))))....))))))....))))))...)))).......... (-35.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUACCAAGACCGUAAAAUUCGACUGAAAAAUAGGAAAUCUGACGCUGGAGCGAUGCUCCUAGGCAGAUUUAUCUUUUUUCCGAGAAUUUAGGUCGGGUUCAAUUCCUUUCUUUUAUAUUGAGUAAUAAAUUUGGGAACCCGUGUUCA ..((.(((..((((...((((((..(.((((((.((((((((((.(.(((((((...))))).)))))))))).))))))))).).)))))).)))).)))))..(((((....(((((........)))))...))))).......... (-39.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 127 82 62 9 smit:SMT_807|5end_hypothetical_protein_predicted_by_Glimmer/Critica_716815..717045_NEGATIVE 316 110 61 162 121 smit:SMT_1723|5end_hypothetical_protein_1709081..1709311_POSITIVE 315 115 73 210 165 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 303 106 64 114 67 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 299 126 81 103 53 smit:SMT_1891|5end_putative_dihydrolipoamide_S-acetyltransferase_1844373..1844603_POSITIVE 299 126 81 103 53 smit:SMT_1402|5end_pyruvate_dehydrogenase_E2_component_(dihydrolipoamide_acetyltransferase)_1378115..1378345_POSITIVE 295 128 81 226 171 smit:SMT_1719|5end_DNA_mismatch_repair_protein_1706842..1707072_NEGATIVE 287 127 82 219 161 smit:SMT_1353|5end_GTP-binding_protein_1331589..1331819_NEGATIVE 286 127 81 183 127 smit:SMT_877|5end_hypothetical_protein_824412..824642_NEGATIVE 284 127 83 228 185 smit:SMT_1541|5end_isopentenyl-diphosphate_delta-isomerase_1526093..1526323_NEGATIVE 284 123 83 196 136 smit:SMT_455|5end_cation_transport_ATPase_391670..391900_POSITIVE 282 128 87 217 167 smit:SMT_1294|5end_K02049_sulfonate/nitrate/taurine_transport_system_ATP-binding_protein_1255983..1256213_POSITIVE 282 109 79 155 112 smit:SMT_936|5end_cobyric_acid_synthase_888669..888899_POSITIVE 279 149 108 53 13 smit:SMT_725|5end_hypothetical_protein_630415..630645_NEGATIVE 277 116 82 229 185 smit:SMT_1354|5end_diacylglycerol_kinase_1332001..1332231_NEGATIVE 275 139 91 160 118 smit:SMT_1807|5end_putative_mucus_binding_protein_1784043..1784273_NEGATIVE 274 129 84 161 116 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 273 116 75 62 20 smit:SMT_1481|5end_endopeptidase_O_1462229..1462459_POSITIVE 272 145 109 159 117 smit:SMT_793|5end_K02029_polar_amino_acid_transport_system_permease_protein_703236..703466_NEGATIVE 269 106 66 159 114 smit:SMT_1931|5end_23S_rRNA_methyltransferase_1870978..1871208_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 531 120 71 56 7 smit:SMT_183|3end_30S_ribosomal_protein_S14_121279..121429_POSITIVE 326 150 103 125 78 smit:SMT_1789|3end_hypothetical_protein_1765511..1765661_POSITIVE 305 117 82 140 111 smit:SMT_410|3end_glucokinase_355477..355627_POSITIVE 286 140 91 69 15 smit:SMT_1728|3end_exodeoxyribonuclease_VII_large_subunit_1714668..1714818_POSITIVE 285 116 81 148 116 smit:SMT_798|3end_hypothetical_protein_707106..707256_POSITIVE 283 130 84 104 55 smit:SMT_1453|3end_K07335_basic_membrane_protein_A_and_related_proteins_1436355..1436505_NEGATIVE 283 140 91 85 34 smit:SMT_1181|3end_phosphotransferase_system,_mannose/fructose-specific_component_IIA_1139413..1139563_NEGATIVE 279 149 108 56 16 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 273 106 82 149 116 smit:SMT_807|3end_hypothetical_protein_predicted_by_Glimmer/Critica_716708..716858_NEGATIVE 272 145 109 150 108 smit:SMT_794|3end_hypothetical_protein_703245..703395_NEGATIVE 265 115 82 54 19 smit:SMT_140|3end_NUDIX_family_hydrolase_91498..91648_POSITIVE 264 137 95 147 102 smit:SMT_543|3end_topoisomerase_IV_subunit_B_460344..460494_POSITIVE 258 115 79 76 49 smit:SMT_1952|3end_hypothetical_protein_1886932..1887082_POSITIVE 257 106 79 150 112 smit:SMT_935|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_888749..888899_POSITIVE 250 127 82 91 44 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 250 127 89 89 50 smit:SMT_1685|3end_phenylalanyl-tRNA_synthetase_alpha_chain_1667757..1667907_NEGATIVE 249 124 81 66 12 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 246 127 81 145 101 smit:SMT_377|3end_hypothetical_protein_315848..315998_POSITIVE 244 129 81 67 3 smit:SMT_1607|3end_K03341_putative_deoxyribonucleotide_triphosphate_pyrophosphatase_1597699..1597849_POSITIVE 244 130 81 110 36 smit:SMT_1494|3end_nucleoside_diphosphate_kinase_1480221..1480371_POSITIVE