Origin IGS: nnnnntacgcggtttgcgaacaattggttaattgtaggcatctacattctcctgtgtttttttatttttggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagatatttttcttttttattgttaattttagctcttttgtagtgctccctaaaaaagaaaaaggaggaatcccaccctcctaaagttagtattgttccattcaatcccatcaattttagcacataatggttttcgagatatgatagta .........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 tactatcatatctcgaaaaccattatgtgctaaaattgatgggattgaatggaacaatactaactttaggagggtgggattcctcctttttcttttttagggagcactacaaaagagctaaaattaacaataaaaaagaaaaatatcttgacaaccaagggaaaattttgttacaataatacacggtactttttacttttggtctctcaagagtgtacagggacgtgctgacaaatgttgcaaaagtacacacagatgatagctgtcaccaagtgtatcatcaccaaaaataaaaaaacacaggagaatgtagatgcctacaattaaccaattgttcgcaaaccgcgtannnnn Mask Tandem Repeat Region ================================================ nnnnntacgcggtttgcgaacaattggttaattgtaggcatctacattctcctgtgtttttttatttttggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagatatttttcttttttattgttaattttagctcttttgtagtgctccctaaaaaagaaaaaggaggaatcccaccctcctaaagttagtattgttccattcaatcccatcaattttagcacataatggttttcgagatatgatagta Find is-nt database================================================ Query_seq: SMT_1083:SMT_1084|SMT_1083:SMT_1084:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:-><-:1021062..1021415 354 nnnnntacgcggtttgcgaacaattggttaattgtaggcatctacattctcctgtgtttttttatttttggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagatatttttcttttttattgttaattttagctcttttgtagtgctccctaaaaaagaaaaaggaggaatcccaccctcctaaagttagtattgttccattcaatcccatcaattttagcacataatggttttcgagatatgatagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1083:SMT_1084|SMT_1083:SMT_1084:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:-><-:1021062..1021415 354 nnnnntacgcggtttgcgaacaattggttaattgtaggcatctacattctcctgtgtttttttatttttggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagatatttttcttttttattgttaattttagctcttttgtagtgctccctaaaaaagaaaaaggaggaatcccaccctcctaaagttagtattgttccattcaatcccatcaattttagcacataatggttttcgagatatgatagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1083:SMT_1084|SMT_1083:SMT_1084:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:-><-:1021062..1021415 354 nnnnntacgcggtttgcgaacaattggttaattgtaggcatctacattctcctgtgtttttttatttttggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagatatttttcttttttattgttaattttagctcttttgtagtgctccctaaaaaagaaaaaggaggaatcccaccctcctaaagttagtattgttccattcaatcccatcaattttagcacataatggttttcgagatatgatagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 nnnnntacgcggtttgcgaacaattggttaattgtaggcatctacattctcctgtgtttttttatttttggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagatatttttcttttttattgttaattttagctcttttgtagtgctccctaaaaaagaaaaaggaggaatcccaccctcctaaagttagtattgttccattcaatcccatcaattttagcacataatggttttcgagatatgatagta Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 31 End: 159 .............................. M V G I Y I L L C F F I F G D D T L G D S Y H L C V L L Q H L S A R P C T L L R D Q K ................................................................................................................................................................................................... Protein_Len: 48 Strand: + Start: 102 End: 245 ..................................................................................................... M C T F A T F V S T S L Y T L E R P K V K S T V Y Y C N K I F P W L S R Y F S F L L L I L A L L ............................................................................................................. Protein_Len: 30 Strand: + Start: 197 End: 286 .................................................................................................................................................................................................... M V V K I F F F F I V N F S S F V V L P K K E K G G I P P S .................................................................... Protein_Len: 31 Strand: - Start: 258 End: 350 ................................................................................................................................................................................................................................................................. F L F L L F G V R R F N T N N W E I G D I K A C L P K R S I M .... Protein_Len: 50 Strand: - Start: 179 End: 328 .................................................................................................................................................................................. Q L L I K G Q N D L Y K E K K N N I K A R K Y H E R F F F F S S D W G G L T L I T G N L G M L K L M .......................... Protein_Len: 50 Strand: - Start: 127 End: 276 .............................................................................................................................. C T G T C E Q S V L L L F Y R T N N Y C F K G K T T L I N K K K I T L K L E K T T S G L F S F P P M .............................................................................. Protein_Len: 30 Strand: - Start: 31 End: 120 .............................. N Y A D V N E Q T K K N K T I I C K T V A I M Q T Y K Q L M .......................................................................................................................................................................................................................................... nnnnntacgcggtttgcgaacaattggttaattgtaggcatctacattctcctgtgtttttttatttttggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagatatttttcttttttattgttaattttagctcttttgtagtgctccctaaaaaagaaaaaggaggaatcccaccctcctaaagttagtattgttccattcaatcccatcaattttagcacataatggttttcgagatatgatagta 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: 82 Start: 321 End: 350 ................................................................................................................................................................................................................................................................................................................................TTTAGCACATAATGGTTTTCGAGATATGAT.... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ nnnnntacgcggtttgcgaacaattggttaattgtaggcatctacattctcctgtgtttttttatttttggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagatatttttcttttttattgttaattttagctcttttgtagtgctccctaaaaaagaaaaaggaggaatcccaccctcctaaagttagtattgttccattcaatcccatcaattttagcacataatggttttcgagatatgatagta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 88 HP_score: -4.8 Tail_Score: -5.75538 Start: 269 End: 286 Full_Region: acaatactaacttta ggaggg tgggat tcctcc tttttcttttttagg ............................................................................................................................................................................................................................................................................ggagggtgggattcctcc.................................................................... Find igs database================================================ Query_seq: SMT_1083:SMT_1084|SMT_1083:SMT_1084:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:-><-:1021062..1021415 354 nnnnntacgcggtttgcgaacaattggttaattgtaggcatctacattctcctgtgtttttttatttttggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagatatttttcttttttattgttaattttagctcttttgtagtgctccctaaaaaagaaaaaggaggaatcccaccctcctaaagttagtattgttccattcaatcccatcaattttagcacataatggttttcgagatatgatagta Intra-Species Hit: Count: 1 Min: 6 Max: 354 Len: 349 Subject: smit_SMT_1083_SMT_1084|hypothetical protein predicted by Glimmer/Critica:hypothetical protein|POSITIVE:NEGATIVE|[1021062,1021415]|354 HSP 1 e-value: 1.0E-117 bit: 422.0 Len: 285 Query Start:70 Query End:354 Subject Strand: POSITIVE Subject Start: 70 Subject End: 354 .....................................................................ggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagatannnnnnnnnnnnattgttaattttagctcttttgtagtgctccctnnnnnnnnnnnnggaggaatcccaccctcctaaagttagtattgttccattcaatcccatcaattttagcacataatggttttcgagatatgatagta .....................................................................ggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagatatttttcttttttattgttaattttagctcttttgtagtgctccctaaaaaagaaaaaggaggaatcccaccctcctaaagttagtattgttccattcaatcccatcaattttagcacataatggttttcgagatatgatagta HSP 2 e-value: 2.0E-20 bit: 101.0 Len: 51 Query Start:6 Query End:56 Subject Strand: POSITIVE Subject Start: 6 Subject End: 56 .....tacgcggtttgcgaacaattggttaattgtaggcatctacattctcctgtg.......................................................................................................................................................................................................................................................................................................... .....tacgcggtttgcgaacaattggttaattgtaggcatctacattctcctgtg.......................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 2 Min: 70 Max: 211 Len: 142 Subject: NC_008533_SPD_0250_SPD_0251|pullulanase, extracellular:ribosomal protein S12|NEGATIVE:POSITIVE|[247146,247561]|416 HSP 1 e-value: 1.0E-67 bit: 258.0 Len: 142 Query Start:70 Query End:211 Subject Strand: NEGATIVE Subject Start: 247 Subject End: 388 .....................................................................ggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagata............................................................................................................................................... .....................................................................ggtgatgatacacttggtgacagatatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtctattattgtaacaaaattttcccttgcttgtcaagata............................................................................................................................................... Subject: NC_003098_spr0247_spr0248|Alkaline amylopullulanase:30S ribosomal protein S12|NEGATIVE:POSITIVE|[247145,247560]|416 HSP 1 e-value: 1.0E-67 bit: 258.0 Len: 142 Query Start:70 Query End:211 Subject Strand: NEGATIVE Subject Start: 247 Subject End: 388 .....................................................................ggtgatgatacacttggtgacagctatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtgtattattgtaacaaaattttcccttggttgtcaagata............................................................................................................................................... .....................................................................ggtgatgatacacttggtgacagatatcatctgtgtgtacttttgcaacatttgtcagcacgtccctgtacactcttgagagaccaaaagtaaaaagtaccgtctattattgtaacaaaattttcccttgcttgtcaagata............................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUGAUGAUACACUUGGUGACAGCUAUCAUCUGUGUGUACUUUUGCAACAUUUGUCAGCACGUCCCUGUACACUCUUGAGAGACCAAAAGUAAAAAGUACCGUGUAUUAUUGUAACAAAAUUUUCCCUUGGUUGUCAAGAUA .(..(((((((((..((.(((.(((..((..(((.((((....)))))))..))..)))..))))).(((((((.(((......))).))).....)))).)))))))))..).............((((.....))))... (-30.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUUGACAACCAAGGGAAAAUUUUGUUACAAUAAUACACGGUACUUUUUACUUUUGGUCUCUCAAGAGUGUACAGGGACGUGCUGACAAAUGUUGCAAAAGUACACACAGAUGAUAGCUGUCACCAAGUGUAUCAUCACC ..((((((..((((((((((((..((((...........))))....)))).))))))))...))))))((((((.(.(((((........))))).)....))))))...((((((((((.......))).)))))))... (-34.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 67 21 66 13 smit:SMT_166|5end_hypothetical_protein_112987..113217_POSITIVE 302 53 18 185 142 smit:SMT_214|5end_leucyl-tRNA_synthetase_146333..146563_POSITIVE 297 46 1 230 176 smit:SMT_2080|5end_glycosyl_transferase_CpsE_1980452..1980682_POSITIVE 297 65 21 61 13 smit:SMT_179|5end_ribosomal_protein_S17_119392..119622_POSITIVE 293 86 43 187 142 smit:SMT_1351|5end_dephospho-CoA_kinase_1329817..1330047_NEGATIVE 292 59 11 167 128 smit:SMT_745|5end_glycosyl_transferase,_group_1_family_protein_650387..650617_NEGATIVE 287 109 61 72 4 smit:SMT_2047|5end_choline_binding_protein_F_1957818..1958048_NEGATIVE 287 70 21 59 2 smit:SMT_1739|5end_hypothetical_protein_1721263..1721493_POSITIVE 281 50 1 64 16 smit:SMT_1296|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1257290..1257520_POSITIVE 274 58 11 152 103 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 273 91 51 52 7 smit:SMT_1007|5end_radical_SAM_domain_protein_947035..947265_POSITIVE 262 64 23 67 21 smit:SMT_945|5end_cytidylate_kinase_895908..896138_NEGATIVE 256 47 3 83 35 smit:SMT_1413|5end_putative_carbon-nitrogen_hydrolase_1397351..1397581_NEGATIVE 250 41 1 179 142 smit:SMT_197|5end_DNA-directed_RNA_polymerase,_alpha_subunit_127686..127916_POSITIVE 249 77 31 57 9 smit:SMT_1481|5end_endopeptidase_O_1462229..1462459_POSITIVE 249 77 31 186 144 smit:SMT_1335|5end_RNA_polymerase_sigma_factor_RpoD_1310201..1310431_NEGATIVE 247 86 41 165 104 smit:SMT_1155|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099665..1099895_NEGATIVE 246 79 36 55 3 smit:SMT_814|5end_UDP-N-acetyl_muramate-alanine_ligase_723666..723896_NEGATIVE 246 66 29 39 2 smit:SMT_176|5end_30S_ribosomal_protein_S3_118081..118311_POSITIVE 244 68 25 59 7 smit:SMT_639|5end_6-phospho-beta-galactosidase_544885..545115_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 67 21 54 1 smit:SMT_165|3end_anaerobic_ribonucleoside-triphosphate_reductase_113055..113205_POSITIVE 286 66 21 64 14 smit:SMT_213|3end_leucyl-tRNA_synthetase_146167..146317_POSITIVE 281 76 31 54 5 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 281 50 1 62 14 smit:SMT_1295|3end_transcriptional_regulator_CtsR_1257368..1257518_POSITIVE 276 84 42 84 44 smit:SMT_362|3end_K02519_translation_initiation_factor_IF-2_297950..298100_POSITIVE 273 91 51 59 14 smit:SMT_1006|3end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_947122..947272_POSITIVE 262 86 42 148 113 smit:SMT_1958|3end_tryptophan_synthase,_beta_subunit_1892052..1892202_POSITIVE 262 64 23 57 11 smit:SMT_946|3end_hypothetical_protein_895918..896068_NEGATIVE 260 92 54 140 90 smit:SMT_1902|3end_proton-translocating_NADH-quinone_oxidoreductase,_chain_L_1852028..1852178_NEGATIVE 260 70 22 57 1 smit:SMT_1738|3end_peptidyl-prolyl_cis-trans_isomerase_1721341..1721491_POSITIVE 259 90 41 59 5 smit:SMT_904|3end_hypothetical_protein_852294..852444_NEGATIVE 256 47 3 73 25 smit:SMT_1414|3end_hypothetical_protein_1397361..1397511_NEGATIVE 250 41 1 136 99 smit:SMT_196|3end_30S_ribosomal_protein_S11_127723..127873_POSITIVE 249 49 16 50 1 smit:SMT_115|3end_hypothetical_protein_66482..66632_POSITIVE 240 59 13 146 90 smit:SMT_339|3end_K03687_molecular_chaperone_GrpE_278490..278640_POSITIVE 239 98 56 54 15 smit:SMT_411|3end_thymidylate_synthase_356415..356565_POSITIVE 237 37 1 81 37 smit:SMT_2165|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2039630..2039780_POSITIVE 230 113 71 143 109 smit:SMT_1192|3end_phosphoribosylaminoimidazolecarboxamide_formyltransferase_/_IMP_cyclohydrolase_1149859..1150009_NEGATIVE 230 46 1 101 59 smit:SMT_445|3end_hypothetical_protein_384949..385099_POSITIVE 228 98 58 89 52 smit:SMT_363|3end_K02519_translation_initiation_factor_IF-2_300751..300901_POSITIVE