Origin IGS: gcgacctgtacggccagcacggtgagtgtaggtttcaatatctctaggaacatcaaagtttacgacacattctaggctatcgannnnnttaattaattaannnnnctat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atagnnnnnttaattaattaannnnntcgatagcctagaatgtgtcgtaaactttgatgttcctagagatattgaaacctacactcaccgtgctggccgtacaggtcgc Mask Tandem Repeat Region ================================================ gcgacctgtacggccagcacggtgagtgtaggtttcaatatctctaggaacatcaaagtttacgacacattctaggctatcgannnnnttaattaattaannnnnctat Find is-nt database================================================ Query_seq: SMT_562:SMT_563|SMT_562:SMT_563:ATP-dependent RNA helicase, DEAD/DEAH box family:thioredoxin reductase:<-->:481019..481127 109 gcgacctgtacggccagcacggtgagtgtaggtttcaatatctctaggaacatcaaagtttacgacacattctaggctatcgannnnnttaattaattaannnnnctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_562:SMT_563|SMT_562:SMT_563:ATP-dependent RNA helicase, DEAD/DEAH box family:thioredoxin reductase:<-->:481019..481127 109 gcgacctgtacggccagcacggtgagtgtaggtttcaatatctctaggaacatcaaagtttacgacacattctaggctatcgannnnnttaattaattaannnnnctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_562:SMT_563|SMT_562:SMT_563:ATP-dependent RNA helicase, DEAD/DEAH box family:thioredoxin reductase:<-->:481019..481127 109 gcgacctgtacggccagcacggtgagtgtaggtttcaatatctctaggaacatcaaagtttacgacacattctaggctatcgannnnnttaattaattaannnnnctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcgacctgtacggccagcacggtgagtgtaggtttcaatatctctaggaacatcaaagtttacgacacattctaggctatcgannnnnttaattaattaannnnnctat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 1 End: 93 R G T R G A R H T Y T E I D R P V D F N V V C E L S D X X X M ................ gcgacctgtacggccagcacggtgagtgtaggtttcaatatctctaggaacatcaaagtttacgacacattctaggctatcgannnnnttaattaattaannnnnctat 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================================================ gcgacctgtacggccagcacggtgagtgtaggtttcaatatctctaggaacatcaaagtttacgacacattctaggctatcgannnnnttaattaattaannnnnctat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_562:SMT_563|SMT_562:SMT_563:ATP-dependent RNA helicase, DEAD/DEAH box family:thioredoxin reductase:<-->:481019..481127 109 gcgacctgtacggccagcacggtgagtgtaggtttcaatatctctaggaacatcaaagtttacgacacattctaggctatcgannnnnttaattaattaannnnnctat Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: smit_SMT_562_SMT_563|ATP-dependent RNA helicase, DEAD/DEAH box family:thioredoxin reductase|NEGATIVE:POSITIVE|[481019,481127]|109 HSP 1 e-value: 2.0E-41 bit: 168.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 gcgacctgtacggccagcacggtgagtgtaggtttcaatatctctaggaacatcaaagtttacgacacattctaggctatcgannnnnttaattaattaa......... gcgacctgtacggccagcacggtgagtgtaggtttcaatatctctaggaacatcaaagtttacgacacattctaggctatcgannnnnttaattaattaa......... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGACCUGUACGGCCAGCACGGUGAGUGUAGGUUUCAAUAUCUCUAGGAACAUCAAAGUUUACGACACAUUCUAGGCUAUCGANNNNNUUAAUUAAUUAA (.(((((((((.(((.....)))..))))))))).)......(((((((...((.........))....)))))))........................ (-15.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUUAAUUAANNNNNUCGAUAGCCUAGAAUGUGUCGUAAACUUUGAUGUUCCUAGAGAUAUUGAAACCUACACUCACCGUGCUGGCCGUACAGGUCGC .................((((((.(((((...(..(((.......)))..)..)))).).))))))......(((.....)))..((((.....)))).. (-17.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1015 50 1 141 92 smit:SMT_562|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_480928..481158_NEGATIVE 306 43 3 203 167 smit:SMT_221|5end_prolyl-tRNA_synthetase_153019..153249_POSITIVE 291 42 2 212 165 smit:SMT_877|5end_hypothetical_protein_824412..824642_NEGATIVE 288 43 10 165 125 smit:SMT_1983|5end_glycerophosphoryl_diester_phosphodiesterase_1913691..1913921_NEGATIVE 281 49 1 139 88 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 279 33 2 200 162 smit:SMT_674|5end_K07010_putative_glutamine_amidotransferase_581561..581791_POSITIVE 278 49 1 69 8 smit:SMT_367|5end_hypothetical_protein_302318..302548_POSITIVE 267 44 1 49 4 smit:SMT_1077|5end_GTP_cyclohydrolase_I_1015410..1015640_NEGATIVE 266 54 15 61 25 smit:SMT_1043|5end_chaperonin_GroEL_985766..985996_NEGATIVE 266 47 2 231 188 smit:SMT_945|5end_cytidylate_kinase_895908..896138_NEGATIVE 261 21 1 58 38 smit:SMT_605|5end_DNA-binding_protein_HU_519034..519264_POSITIVE 260 50 1 109 54 smit:SMT_611|5end_aspartate-semialdehyde_dehydrogenase_522492..522722_POSITIVE 259 36 2 103 64 smit:SMT_2097|5end_type_I_restriction_enzyme_M_protein_1991272..1991502_NEGATIVE 257 48 1 115 63 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 256 48 6 104 49 smit:SMT_852|5end_K03978_GTP-binding_protein_798044..798274_NEGATIVE 255 48 1 186 143 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 255 50 1 107 38 smit:SMT_1174|5end_acylneuraminate_cytidylyltransferase_1126321..1126551_NEGATIVE 255 45 1 95 45 smit:SMT_1173|5end_CMP-N-acetylneuraminate-beta-galactosamide-alpha_-2,3-sialyltransferase_1125620..1125850_NEGATIVE 254 47 5 99 49 smit:SMT_662|5end_A/G-specific_adenine_glycosylase_573827..574057_NEGATIVE 250 49 1 225 171 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 47 3 105 50 smit:SMT_1631|3end_phosphopantothenoylcysteine_synthase/decarboxylase_1618204..1618354_NEGATIVE 288 43 10 151 111 smit:SMT_1984|3end_phosphinothricin_N-acetyltransferase_1913705..1913855_NEGATIVE 278 36 3 137 94 smit:SMT_1957|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1890829..1890979_POSITIVE 278 49 1 69 8 smit:SMT_366|3end_hypothetical_protein_302398..302548_POSITIVE 273 49 3 76 9 smit:SMT_957|3end_UDP-glucose_4-epimerase_904776..904926_NEGATIVE 267 44 1 68 23 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 263 48 2 151 110 smit:SMT_890|3end_K02029_polar_amino_acid_transport_system_permease_protein_837692..837842_POSITIVE 256 48 6 95 40 smit:SMT_853|3end_ATP-dependent_endopeptidase_clp_ATP-binding_subunit_ClpX_798053..798203_NEGATIVE 255 50 1 123 54 smit:SMT_1175|3end_K03307_solute:Na+_symporter,_SSS_family_1126305..1126455_NEGATIVE 255 45 1 98 48 smit:SMT_1174|3end_acylneuraminate_cytidylyltransferase_1125617..1125767_NEGATIVE 252 49 3 143 94 smit:SMT_1886|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1841198..1841348_POSITIVE 249 38 3 96 52 smit:SMT_1955|3end_carbamoyl-phosphate_synthase_small_chain_1888992..1889142_NEGATIVE 249 28 1 56 26 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 249 33 3 134 94 smit:SMT_1155|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099183..1099333_NEGATIVE 248 36 1 48 14 smit:SMT_255|3end_K02026_multiple_sugar_transport_system_permease_protein_192707..192857_POSITIVE 247 50 1 73 17 smit:SMT_1953|3end_hypothetical_protein_1888107..1888257_POSITIVE 247 49 1 67 17 smit:SMT_1006|3end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_947122..947272_POSITIVE 247 37 3 149 104 smit:SMT_542|3end_hypothetical_protein_458400..458550_POSITIVE 246 44 3 147 94 smit:SMT_2026|3end_K03466_DNA_segregation_ATPase_FtsK/SpoIIIE,_S-DNA-T_family_1941905..1942055_NEGATIVE 246 50 1 76 17 smit:SMT_513|3end_16S_rRNA_processing_protein_RimM_441467..441617_POSITIVE