Origin IGS: tagcatagccaaaaaatcgttacatgtcgtaacgattttttcatttagccgatgacagtaaaggtcatacaattttgggaagagcaagtatactatcatagtgtgcaaaatactgaagaagtgtttgctcaggcgtttccctataacttatcataagcgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcgcttatgataagttatagggaaacgcctgagcaaacacttcttcagtattttgcacactatgatagtatacttgctcttcccaaaattgtatgacctttactgtcatcggctaaatgaaaaaatcgttacgacatgtaacgattttttggctatgcta Mask Tandem Repeat Region ================================================ tagcatagccaaaaaatcgttacatgtcgtaacgattttttcatttagccgatgacagtaaaggtcatacaattttgggaagagcaagtatactatcatagtgtgcaaaatactgaagaagtgtttgctcaggcgtttccctataacttatcataagcgc Find is-nt database================================================ Query_seq: SSA_0357:SSA_0358|SSA_0357:SSA_0358:Thioredoxin, putative:hypothetical protein:-><-:351218..351377 160 tagcatagccaaaaaatcgttacatgtcgtaacgattttttcatttagccgatgacagtaaaggtcatacaattttgggaagagcaagtatactatcatagtgtgcaaaatactgaagaagtgtttgctcaggcgtttccctataacttatcataagcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0357:SSA_0358|SSA_0357:SSA_0358:Thioredoxin, putative:hypothetical protein:-><-:351218..351377 160 tagcatagccaaaaaatcgttacatgtcgtaacgattttttcatttagccgatgacagtaaaggtcatacaattttgggaagagcaagtatactatcatagtgtgcaaaatactgaagaagtgtttgctcaggcgtttccctataacttatcataagcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0357:SSA_0358|SSA_0357:SSA_0358:Thioredoxin, putative:hypothetical protein:-><-:351218..351377 160 tagcatagccaaaaaatcgttacatgtcgtaacgattttttcatttagccgatgacagtaaaggtcatacaattttgggaagagcaagtatactatcatagtgtgcaaaatactgaagaagtgtttgctcaggcgtttccctataacttatcataagcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagcatagccaaaaaatcgttacatgtcgtaacgattttttcatttagccgatgacagtaaaggtcatacaattttgggaagagcaagtatactatcatagtgtgcaaaatactgaagaagtgtttgctcaggcgtttccctataacttatcataagcgc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 52 End: 153 ................................................... M T V K V I Q F W E E Q V Y Y H S V Q N T E E V F A Q A F P Y N L S ....... Protein_Len: 48 Strand: - Start: 1 End: 144 L M A L F D N C T T V I K E N L R H C Y L D Y L K P F L L Y V I M T H L I S F F H K S L R K G M ................ tagcatagccaaaaaatcgttacatgtcgtaacgattttttcatttagccgatgacagtaaaggtcatacaattttgggaagagcaagtatactatcatagtgtgcaaaatactgaagaagtgtttgctcaggcgtttccctataacttatcataagcgc 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================================================ tagcatagccaaaaaatcgttacatgtcgtaacgattttttcatttagccgatgacagtaaaggtcatacaattttgggaagagcaagtatactatcatagtgtgcaaaatactgaagaagtgtttgctcaggcgtttccctataacttatcataagcgc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 91 HP_score: -8.2 Tail_Score: -5.13473 Start: 17 End: 35 Full_Region: ggctaaatgaaaaaa tcgttacg aca tgtaacga ttttttggctatgct ................tcgttacgacatgtaacga............................................................................................................................. Find igs database================================================ Query_seq: SSA_0357:SSA_0358|SSA_0357:SSA_0358:Thioredoxin, putative:hypothetical protein:-><-:351218..351377 160 tagcatagccaaaaaatcgttacatgtcgtaacgattttttcatttagccgatgacagtaaaggtcatacaattttgggaagagcaagtatactatcatagtgtgcaaaatactgaagaagtgtttgctcaggcgtttccctataacttatcataagcgc Intra-Species Hit: Count: 1 Min: 1 Max: 160 Len: 160 Subject: NC_009009_SSA_0357_SSA_0358|Thioredoxin, putative:hypothetical protein|POSITIVE:NEGATIVE|[351218,351377]|160 HSP 1 e-value: 6.0E-86 bit: 317.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 tagcatagccaaaaaatcgttacatgtcgtaacgattttttcatttagccgatgacagtaaaggtcatacaattttgggaagagcaagtatactatcatagtgtgcaaaatactgaagaagtgtttgctcaggcgtttccctataacttatcataagcgc tagcatagccaaaaaatcgttacatgtcgtaacgattttttcatttagccgatgacagtaaaggtcatacaattttgggaagagcaagtatactatcatagtgtgcaaaatactgaagaagtgtttgctcaggcgtttccctataacttatcataagcgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAUAGCCAAAAAAUCGUUACAUGUCGUAACGAUUUUUUCAUUUAGCCGAUGACAGUAAAGGUCAUACAAUUUUGGGAAGAGCAAGUAUACUAUCAUAGUGUGCAAAAUACUGAAGAAGUGUUUGCUCAGGCGUUUCCCUAUAACUUAUCAUAAGCGC ..((......(((((((((((((.....)))))))))))))......(((.(((((.......))))).............((((..((((((((...)))))))).(((((((.....))))))))))).)))......................)).. (-42.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGCUUAUGAUAAGUUAUAGGGAAACGCCUGAGCAAACACUUCUUCAGUAUUUUGCACACUAUGAUAGUAUACUUGCUCUUCCCAAAAUUGUAUGACCUUUACUGUCAUCGGCUAAAUGAAAAAAUCGUUACGACAUGUAACGAUUUUUUGGCUAUGCUA ((.(((((((....))))))).....(((...(((((.(((.....)))..))))).....(((((((((....(((.............))).......))))))))).)))....(.(((((((((((((.....))))))))))))).)....)).. (-35.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 143 103 58 16 NC_009009:SSA_1911|5end_Conserved_uncharacterized_protein_1903105..1903335_NEGATIVE 285 90 41 161 105 NC_009009:SSA_0758|5end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_740636..740866_POSITIVE 274 160 120 204 158 NC_009009:SSA_2033|5end_30S_ribosomal_protein_S9,_putative_2038779..2039009_NEGATIVE 273 149 102 177 128 NC_009009:SSA_0390|5end_hypothetical_protein_385002..385232_POSITIVE 270 144 102 190 139 NC_009009:SSA_1082|5end_PTS_system,_fructose_specific_II_ABC_components,_putative_1099186..1099416_POSITIVE 270 87 48 208 169 NC_009009:SSA_0291|5end_Oxidoreductase,_putative_285362..285592_POSITIVE 269 135 95 129 87 NC_009009:SSA_2192|5end_Conserved_uncharacterized_protein_2193842..2194072_NEGATIVE 267 138 98 54 21 NC_009009:SSA_1428|5end_hypothetical_protein_1436348..1436578_NEGATIVE 264 160 123 210 171 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 264 69 24 82 40 NC_009009:SSA_0814|5end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_796835..797065_NEGATIVE 263 136 97 166 120 NC_009009:SSA_0743|5end_Transcriptional_repressor_(arginine_synthesis),_putative_725759..725989_NEGATIVE 262 69 23 85 28 NC_009009:SSA_1353|5end_hypothetical_protein_1368519..1368749_NEGATIVE 256 160 113 219 180 NC_009009:SSA_2042|5end_hypothetical_protein_2047073..2047303_NEGATIVE 256 90 47 168 125 NC_009009:SSA_1668|5end_NrdI_protein,_putative_1668091..1668321_NEGATIVE 252 160 115 59 3 NC_009009:SSA_2264|5end_hypothetical_protein_2261757..2261987_NEGATIVE 252 41 2 101 54 NC_009009:SSA_0708|5end_hypothetical_protein_694144..694374_POSITIVE 249 139 100 183 144 NC_009009:SSA_1180|5end_hypothetical_protein_1208559..1208789_NEGATIVE 246 108 63 120 68 NC_009009:SSA_0669|5end_ATP_dependent_protease,_putative_653720..653950_NEGATIVE 245 160 113 191 133 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 244 70 38 30 1 NC_009009:SSA_1786|5end_Conserved_uncharacterized_protein_1770244..1770474_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 143 103 50 8 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 285 90 41 143 87 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 267 138 98 47 14 NC_009009:SSA_1429|3end_hypothetical_protein_1436355..1436505_NEGATIVE 264 160 123 112 73 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 263 136 97 149 103 NC_009009:SSA_0744|3end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_725776..725926_NEGATIVE 256 139 93 44 8 NC_009009:SSA_0728|3end_Protease,_putative_714523..714673_POSITIVE 253 65 23 129 82 NC_009009:SSA_0948|3end_hypothetical_protein_955628..955778_POSITIVE 249 139 100 150 111 NC_009009:SSA_1181|3end_Hydrolase,_alpha/beta_superfamily,_putative_1208592..1208742_NEGATIVE 245 160 113 106 48 NC_009009:SSA_1368|3end_hypothetical_protein_1383748..1383898_NEGATIVE 241 150 101 87 34 NC_009009:SSA_0532|3end_Propanediol_utilization_protein_PduB,_putative_529028..529178_POSITIVE 239 69 22 147 101 NC_009009:SSA_1581|3end_Metal-binding_ABC_transporter_(probably_hemin),_putative_1584770..1584920_POSITIVE 236 86 47 142 100 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 235 135 94 74 30 NC_009009:SSA_0110|3end_50S_ribosomal_protein_L2,_putative_110666..110816_POSITIVE 232 99 56 57 3 NC_009009:SSA_0201|3end_ABC_multidrug_transporter_(3-component_subtilin_immunity_exporter),_putative_200612..200762_POSITIVE 229 90 48 88 36 NC_009009:SSA_1871|3end_Penicillin-binding_protein_2X,_putative_1866585..1866735_NEGATIVE 228 159 125 135 98 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 228 56 11 95 50 NC_009009:SSA_0357|3end_Thioredoxin,_putative_351157..351307_POSITIVE 224 143 102 124 84 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 222 159 129 120 91 NC_009009:SSA_0784|3end_Proton-translocating_ATPase,_F0_sector,_subunit_b,_putative_768124..768274_POSITIVE 219 44 2 76 16 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE