Origin IGS: agttactctcgctgcttgaccaagtcctccgattggggaaccttagccttgtcaaacaaagcaactccataaccaagagctacaccagcaccaaaaagtccaccgataaagcctagaataaagagagtannnnnttaattaattaannnnntacagatgctgcatttgtaagagctgaacgactcactttaactgggtcgatatcccctgatcaatcatgtaaacccattcgccagttgctgcattgaagcctgtacmacttcagcatttt .........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 aaaatgctgaagtkgtacaggcttcaatgcagcaactggcgaatgggtttacatgattgatcaggggatatcgacccagttaaagtgagtcgttcagctcttacaaatgcagcatctgtannnnnttaattaattaannnnntactctctttattctaggctttatcggtggactttttggtgctggtgtagctcttggttatggagttgctttgtttgacaaggctaaggttccccaatcggaggacttggtcaagcagcgagagtaact Mask Tandem Repeat Region ================================================ agttactctcgctgcttgaccaagtcctccgattggggaaccttagccttgtcaaacaaagcaactccataaccaagagctacaccagcaccaaaaagtccaccgataaagcctagaataaagagagtannnnnttaattaattaannnnntacagatgctgcatttgtaagagctgaacgactcactttaactgggtcgatatcccctgatcaatcatgtaaacccattcgccagttgctgcattgaagcctgtacmacttcagcatttt Find is-nt database================================================ Query_seq: SMT_1043:SMT_1044|SMT_1043:SMT_1044:chaperonin GroEL:chaperonin GroEL (HSP60 family):<-<-:985857..986127 271 agttactctcgctgcttgaccaagtcctccgattggggaaccttagccttgtcaaacaaagcaactccataaccaagagctacaccagcaccaaaaagtccaccgataaagcctagaataaagagagtannnnnttaattaattaannnnntacagatgctgcatttgtaagagctgaacgactcactttaactgggtcgatatcccctgatcaatcatgtaaacccattcgccagttgctgcattgaagcctgtacmacttcagcatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1043:SMT_1044|SMT_1043:SMT_1044:chaperonin GroEL:chaperonin GroEL (HSP60 family):<-<-:985857..986127 271 agttactctcgctgcttgaccaagtcctccgattggggaaccttagccttgtcaaacaaagcaactccataaccaagagctacaccagcaccaaaaagtccaccgataaagcctagaataaagagagtannnnnttaattaattaannnnntacagatgctgcatttgtaagagctgaacgactcactttaactgggtcgatatcccctgatcaatcatgtaaacccattcgccagttgctgcattgaagcctgtacmacttcagcatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1043:SMT_1044|SMT_1043:SMT_1044:chaperonin GroEL:chaperonin GroEL (HSP60 family):<-<-:985857..986127 271 agttactctcgctgcttgaccaagtcctccgattggggaaccttagccttgtcaaacaaagcaactccataaccaagagctacaccagcaccaaaaagtccaccgataaagcctagaataaagagagtannnnnttaattaattaannnnntacagatgctgcatttgtaagagctgaacgactcactttaactgggtcgatatcccctgatcaatcatgtaaacccattcgccagttgctgcattgaagcctgtacmacttcagcatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agttactctcgctgcttgaccaagtcctccgattggggaaccttagccttgtcaaacaaagcaactccataaccaagagctacaccagcaccaaaaagtccaccgataaagcctagaataaagagagtannnnnttaattaattaannnnntacagatgctgcatttgtaagagctgaacgactcactttaactgggtcgatatcccctgatcaatcatgtaaacccattcgccagttgctgcattgaagcctgtacmacttcagcatttt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 12 End: 113 ........... M L D Q V L R L G N L S L V K Q S N S I T K S Y T S T K K S T D K A .............................................................................................................................................................. Protein_Len: 39 Strand: - Start: 6 End: 119 ..... * E R Q K V L D E S Q P V K A K D F L A V G Y G L A V G A G F L G G I F G L M ........................................................................................................................................................ agttactctcgctgcttgaccaagtcctccgattggggaaccttagccttgtcaaacaaagcaactccataaccaagagctacaccagcaccaaaaagtccaccgataaagcctagaataaagagagtannnnnttaattaattaannnnntacagatgctgcatttgtaagagctgaacgactcactttaactgggtcgatatcccctgatcaatcatgtaaacccattcgccagttgctgcattgaagcctgtacmacttcagcatttt 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================================================ agttactctcgctgcttgaccaagtcctccgattggggaaccttagccttgtcaaacaaagcaactccataaccaagagctacaccagcaccaaaaagtccaccgataaagcctagaataaagagagtannnnnttaattaattaannnnntacagatgctgcatttgtaagagctgaacgactcactttaactgggtcgatatcccctgatcaatcatgtaaacccattcgccagttgctgcattgaagcctgtacmacttcagcatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1043:SMT_1044|SMT_1043:SMT_1044:chaperonin GroEL:chaperonin GroEL (HSP60 family):<-<-:985857..986127 271 agttactctcgctgcttgaccaagtcctccgattggggaaccttagccttgtcaaacaaagcaactccataaccaagagctacaccagcaccaaaaagtccaccgataaagcctagaataaagagagtannnnnttaattaattaannnnntacagatgctgcatttgtaagagctgaacgactcactttaactgggtcgatatcccctgatcaatcatgtaaacccattcgccagttgctgcattgaagcctgtacmacttcagcatttt Intra-Species Hit: Count: 1 Min: 1 Max: 271 Len: 271 Subject: smit_SMT_1043_SMT_1044|chaperonin GroEL:chaperonin GroEL (HSP60 family)|NEGATIVE:NEGATIVE|[985857,986127]|271 HSP 1 e-value: 1.0E-133 bit: 475.0 Len: 271 Query Start:1 Query End:271 Subject Strand: POSITIVE Subject Start: 1 Subject End: 271 agttactctcgctgcttgaccaagtcctccgattggggaaccttagccttgtcaaacaaagcaactccataaccaagagctacaccagcaccaaaaagtccaccgataaagcctagaataaagagagtannnnnttaattaattaannnnntacagatgctgcatttgtaagagctgaacgactcactttaactgggtcgatatcccctgatcaatcatgtaaacccattcgccagttgctgcattgaagcctgtacmacttcagcatttt agttactctcgctgcttgaccaagtcctccgattggggaaccttagccttgtcaaacaaagcaactccataaccaagagctacaccagcaccaaaaagtccaccgataaagcctagaataaagagagtannnnnttaattaattaannnnntacagatgctgcatttgtaagagctgaacgactcactttaactgggtcgatatcccctgatcaatcatgtaaacccattcgccagttgctgcattgaagcctgtacmacttcagcatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUACUCUCGCUGCUUGACCAAGUCCUCCGAUUGGGGAACCUUAGCCUUGUCAAACAAAGCAACUCCAUAACCAAGAGCUACACCAGCACCAAAAAGUCCACCGAUAAAGCCUAGAAUAAAGAGAGUANNNNNUUAAUUAAUUAANNNNNUACAGAUGCUGCAUUUGUAAGAGCUGAACGACUCACUUUAACUGGGUCGAUAUCCCCUGAUCAAUCAUGUAAACCCAUUCGCCAGUUGCUGCAUUGAAGCCUGUACMACUUCAGCAUUUU ...(((((((...((((....))))......((((((((......((.(((.....))).))................(((.....))).........))).)))))...............)))))))......................((((((((...))))))))...(((((((((((((.......)))))))...........(((((((.((((...(....)....)))))).)))))............))))))..... (-50.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGCUGAAGUKGUACAGGCUUCAAUGCAGCAACUGGCGAAUGGGUUUACAUGAUUGAUCAGGGGAUAUCGACCCAGUUAAAGUGAGUCGUUCAGCUCUUACAAAUGCAGCAUCUGUANNNNNUUAAUUAAUUAANNNNNUACUCUCUUUAUUCUAGGCUUUAUCGGUGGACUUUUUGGUGCUGGUGUAGCUCUUGGUUAUGGAGUUGCUUUGUUUGACAAGGCUAAGGUUCCCCAAUCGGAGGACUUGGUCAAGCAGCGAGAGUAACU ...((((.(((((.......)))))..((((..(((((((((....(((..(.(((....))))..))).)))..))))))...(((((.(.....)..)))))...))))))))...........................(((((((...............((((((..(((....)))))))))((((((((.......))))))))..((((((((.......((((((.((....)).)))))).))))))))..)))))))... (-65.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1020 50 1 141 92 smit:SMT_1043|5end_chaperonin_GroEL_985766..985996_NEGATIVE 391 90 41 54 12 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 353 270 231 198 154 smit:SMT_1756|5end_hypothetical_protein_1734170..1734400_NEGATIVE 341 79 31 79 12 smit:SMT_1823|5end_GTP-binding_protein_1794982..1795212_POSITIVE 334 90 45 110 52 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 333 47 2 209 157 smit:SMT_1264|5end_oligoendopeptidase_F_1228858..1229088_POSITIVE 325 118 75 42 8 smit:SMT_1307|5end_glycerol_uptake_facilitator_protein_1271664..1271894_POSITIVE 324 235 193 36 1 smit:SMT_1933|5end_K02006_cobalt_transport_system_ATP-binding_protein_1872222..1872452_NEGATIVE 317 210 171 66 9 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 317 80 33 67 15 smit:SMT_243|5end_PTS_system,_mannose-specific_IIC_component_180901..181131_NEGATIVE 308 54 15 47 1 smit:SMT_866|5end_50S_ribosomal_protein_L11_816234..816464_NEGATIVE 303 68 21 186 145 smit:SMT_574|5end_PTS_system,_fructose_specific_IIABC_components_491884..492114_POSITIVE 301 47 1 230 178 smit:SMT_1478|5end_manganese_transport_system_membrane_protein_1461256..1461486_NEGATIVE 297 239 192 65 23 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 295 49 6 170 112 smit:SMT_748|5end_prephenate_dehydratase_653498..653728_NEGATIVE 292 62 28 168 137 smit:SMT_416|5end_ribonuclease_Z_359423..359653_POSITIVE 291 54 11 78 36 smit:SMT_1124|5end_pyrrolidone-carboxylate_peptidase_1060869..1061099_NEGATIVE 291 48 10 225 182 smit:SMT_166|5end_hypothetical_protein_112987..113217_POSITIVE 290 39 7 204 164 smit:SMT_639|5end_6-phospho-beta-galactosidase_544885..545115_NEGATIVE 290 89 42 196 140 smit:SMT_355|5end_hypothetical_protein_291622..291852_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 341 79 31 76 9 smit:SMT_1822|3end_hypothetical_protein_1795059..1795209_POSITIVE 334 90 45 67 9 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 317 55 11 146 101 smit:SMT_121|3end_hypothetical_protein_74414..74564_POSITIVE 313 54 11 69 23 smit:SMT_1580|3end_MutT/NUDIX_family_protein_1573153..1573303_POSITIVE 306 106 62 128 88 smit:SMT_1857|3end_hypothetical_protein_1821145..1821295_POSITIVE 304 210 175 54 13 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 297 239 192 102 60 smit:SMT_1695|3end_ribulose-phosphate_3-epimerase_1678299..1678449_POSITIVE 297 266 223 47 8 smit:SMT_140|3end_NUDIX_family_hydrolase_91498..91648_POSITIVE 296 266 228 132 97 smit:SMT_1279|3end_translation_elongation_factor_Ts_1243451..1243601_POSITIVE 294 177 159 131 113 smit:SMT_1363|3end_50S_ribosomal_protein_L20_1343254..1343404_NEGATIVE 289 47 2 81 34 smit:SMT_1069|3end_acetyl_xylan_esterase,_putative_1009595..1009745_POSITIVE 287 267 224 148 95 smit:SMT_1222|3end_pneumococcal_surface_protein_A_1185683..1185833_NEGATIVE 286 244 205 61 21 smit:SMT_1979|3end_possible_cell_surface_protein_1910282..1910432_NEGATIVE 283 208 162 106 58 smit:SMT_1483|3end_GTP-binding_protein_1463140..1463290_NEGATIVE 282 48 4 141 105 smit:SMT_1627|3end_hypothetical_protein_1616089..1616239_NEGATIVE 281 256 224 89 56 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 280 49 9 151 105 smit:SMT_1690|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1673370..1673520_NEGATIVE 280 248 201 139 83 smit:SMT_723|3end_hypothetical_protein_629116..629266_NEGATIVE 279 59 12 90 37 smit:SMT_2073|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1977074..1977224_POSITIVE 277 54 11 145 110 smit:SMT_415|3end_hypothetical_protein_359488..359638_POSITIVE