Origin IGS: cgataatctctccattttcattatcagtctaatgtaaataagcacgtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagtagatgttcagccaatgcgacgaggtaggaccaaaggtcgataaggtgtgttctgggtataggactctttaaagtaagtaggaaatatgatgagatgatacagagagcctgaattggtcaggtgacgtgcttatttacattagactgataatgaaaatggagagattatcg Mask Tandem Repeat Region ================================================ cgataatctctccattttcattatcagtctaatgtaaataagcacgtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt Find is-nt database================================================ Query_seq: SMT_1442:SMT_1443|SMT_1442:SMT_1443:hypothetical protein:23S rRNA m(5)U 1939 methyltransferase:<-<-:1426419..1426592 174 cgataatctctccattttcattatcagtctaatgtaaataagcacgtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1442:SMT_1443|SMT_1442:SMT_1443:hypothetical protein:23S rRNA m(5)U 1939 methyltransferase:<-<-:1426419..1426592 174 cgataatctctccattttcattatcagtctaatgtaaataagcacgtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1442:SMT_1443|SMT_1442:SMT_1443:hypothetical protein:23S rRNA m(5)U 1939 methyltransferase:<-<-:1426419..1426592 174 cgataatctctccattttcattatcagtctaatgtaaataagcacgtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgataatctctccattttcattatcagtctaatgtaaataagcacgtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 51 End: 161 .................................................. M T N S G S L Y H L I I F P T Y F K E S Y T Q N T P Y R P L V L P R R I G ............. Protein_Len: 39 Strand: + Start: 58 End: 174 ......................................................... M Q A L C I I S S Y F L L T L K S P I P R T H L I D L W S Y L V A L A E H L L cgataatctctccattttcattatcagtctaatgtaaataagcacgtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt 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================================================ cgataatctctccattttcattatcagtctaatgtaaataagcacgtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1442:SMT_1443|SMT_1442:SMT_1443:hypothetical protein:23S rRNA m(5)U 1939 methyltransferase:<-<-:1426419..1426592 174 cgataatctctccattttcattatcagtctaatgtaaataagcacgtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: smit_SMT_1442_SMT_1443|hypothetical protein:23S rRNA m(5)U 1939 methyltransferase|NEGATIVE:NEGATIVE|[1426419, 1426592]|174 HSP 1 e-value: 3.0E-94 bit: 345.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 cgataatctctccattttcattatcagtctaatgtaaataagcacgtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt cgataatctctccattttcattatcagtctaatgtaaataagcacgtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt Inter-species Hit: Count: 3 Min: 46 Max: 174 Len: 129 Subject: NC_008533_SPD_0921_SPD_0922|site-specific recombinase, resolvase family protein:hypothetical protein|POSITIVE:POSITIVE|[935267,935488]|222 HSP 1 e-value: 4.0E-53 bit: 208.0 Len: 129 Query Start:46 Query End:174 Subject Strand: NEGATIVE Subject Start: 95 Subject End: 222 .............................................gtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt .............................................gtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttac-gagtcctatacccagaacacaccttatcgaccttcggtctcacctcgtcgcattggctgaacatctactt Subject: NC_003098_spr0942_spr0943|Low similarity to site-specific recombinase:hypothetical protein|POSITIVE:POSITIVE|[927736,927957]|222 HSP 1 e-value: 4.0E-53 bit: 208.0 Len: 129 Query Start:46 Query End:174 Subject Strand: NEGATIVE Subject Start: 95 Subject End: 222 .............................................gtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt .............................................gtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttac-gagtcctatacccagaacacaccttatcgaccttcggtctcacctcgtcgcattggctgaacatctactt Subject: NC_003028_SP_1040_SP_1041|site-specific recombinase, resolvase family:hypothetical protein|POSITIVE:POSITIVE|[980903,981124]|222 HSP 1 e-value: 1.0E-50 bit: 200.0 Len: 129 Query Start:46 Query End:174 Subject Strand: NEGATIVE Subject Start: 95 Subject End: 222 .............................................gtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttactttaaagagtcctatacccagaacacaccttatcgacctttggtcctacctcgtcgcattggctgaacatctactt .............................................gtcacctgaccaattcaggctctctgtatcatctcatcatatttcctacttacttt-acgagtcttatacccagaacacaccttatcgaccttcggtctcacctcgtcgcattggctgaacatctactt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCACCUGACCAAUUCAGGCUCUCUGUAUCAUCUCAUCAUAUUUCCUACUUACUUUAAAGAGUCCUAUACCCAGAACACACCUUAUCGACCUUUGGUCCUACCUCGUCGCAUUGGCUGAACAUCUACUU ....(((((.....))))).(((..((((...(((........................)))....))))..)))...((((....((((....((.....))..))))....)).))........... (-16.66) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAGAUGUUCAGCCAAUGCGACGAGGUAGGACCAAAGGUCGAUAAGGUGUGUUCUGGGUAUAGGACUCUUUAAAGUAAGUAGGAAAUAUGAUGAGAUGAUACAGAGAGCCUGAAUUGGUCAGGUGAC ..(((....((((.((.((...((.......((((...))))..(((((...((((((....)))))).)))))..))..)).))........))))....))).....((((((.....))))))... (-25.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 909 50 1 186 137 smit:SMT_1442|5end_hypothetical_protein_1426328..1426558_NEGATIVE 323 120 87 157 123 smit:SMT_1738|5end_peptidyl-prolyl_cis-trans_isomerase_1720497..1720727_POSITIVE 319 109 61 123 85 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 312 120 85 86 44 smit:SMT_489|5end_K01999_branched-chain_amino_acid_transport_system_substrate-binding_protein_423669..423899_POSITIVE 311 106 80 140 114 smit:SMT_1943|5end_alpha/beta_hydrolase_fold_1878968..1879198_NEGATIVE 298 57 14 86 39 smit:SMT_1526|5end_K07720_two-component_system,_response_regulator_YesN_1510554..1510784_NEGATIVE 271 97 60 188 144 smit:SMT_1509|5end_phosphopentomutase_1492781..1493011_NEGATIVE 270 119 85 183 158 smit:SMT_1986|5end_mercuric_reductase_1914843..1915073_POSITIVE 270 119 85 216 191 smit:SMT_325|5end_K02029_polar_amino_acid_transport_system_permease_protein_263023..263253_NEGATIVE 268 116 88 63 28 smit:SMT_764|5end_alanyl-tRNA_synthetase_672113..672343_NEGATIVE 267 117 71 116 55 smit:SMT_1466|5end_endopeptidase_O_1446962..1447192_POSITIVE 267 119 84 79 40 smit:SMT_1457|5end_16S_rRNA_m(2)G_1207_methyltransferase_1440209..1440439_NEGATIVE 263 105 61 102 44 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 262 46 9 103 66 smit:SMT_2075|5end_phosphoribosylamine--glycine_ligase_1978485..1978715_NEGATIVE 262 119 82 133 87 smit:SMT_993|5end_hypothetical_protein_935476..935706_NEGATIVE 261 119 71 75 24 smit:SMT_520|5end_glutathione_reductase_445285..445515_NEGATIVE 259 50 13 105 68 smit:SMT_338|5end_heat-inducible_transcription_repressor_HrcA_276825..277055_POSITIVE 257 118 73 198 141 smit:SMT_1068|5end_ATP-dependent_DNA_helicase_RecG_1006891..1007121_POSITIVE 257 118 71 207 154 smit:SMT_368|5end_hypothetical_protein_303662..303892_POSITIVE 256 119 74 130 96 smit:SMT_2059|5end_hypothetical_protein_1967881..1968111_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 109 61 121 83 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 311 106 80 33 7 smit:SMT_1944|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1879075..1879225_NEGATIVE 298 57 14 74 27 smit:SMT_1527|3end_two-component_sensor_kinase_1510566..1510716_NEGATIVE 268 116 88 41 6 smit:SMT_765|3end_hypothetical_protein_672135..672285_NEGATIVE 262 46 9 106 69 smit:SMT_2076|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1978482..1978632_NEGATIVE 262 119 82 133 87 smit:SMT_994|3end_nicotinate-nucleotide_adenylyltransferase_935476..935626_NEGATIVE 259 120 81 148 111 smit:SMT_2067|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1974216..1974366_POSITIVE 255 108 62 72 12 smit:SMT_1251|3end_hypothetical_protein_1211329..1211479_NEGATIVE 252 117 74 47 4 smit:SMT_110|3end_alpha-L-fucosidase_59207..59357_POSITIVE 249 97 57 77 42 smit:SMT_2054|3end_dTDP-glucose_4,6-dehydratase_1965767..1965917_POSITIVE 244 120 72 133 67 smit:SMT_668|3end_hypothetical_protein_predicted_by_Glimmer/Critica_578057..578207_NEGATIVE 243 119 72 67 24 smit:SMT_1069|3end_acetyl_xylan_esterase,_putative_1009595..1009745_POSITIVE 242 47 2 91 48 smit:SMT_805|3end_hypothetical_protein_predicted_by_Glimmer/Critica_715692..715842_NEGATIVE 240 110 62 118 68 smit:SMT_1041|3end_K07586_hypothetical_protein_984164..984314_POSITIVE 238 50 10 139 101 smit:SMT_812|3end_acetyltransferase,_GNAT_family_721664..721814_NEGATIVE 235 119 98 22 1 smit:SMT_1852|3end_1,4-alpha-glucan_branching_enzyme_1816467..1816617_NEGATIVE 235 119 98 22 1 smit:SMT_326|3end_K02029_polar_amino_acid_transport_system_permease_protein_263217..263367_NEGATIVE 234 120 71 80 32 smit:SMT_108|3end_hypothetical_protein_53873..54023_POSITIVE 233 117 87 136 104 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 233 109 61 140 93 smit:SMT_1244|3end_putative_repressor_protein_1205149..1205299_POSITIVE