Origin IGS: aacaataaaaagttctcgaagtcgagaactttttttgtgcatgtataatgaaatccatcaacaaactagaaagtcagctgctgaagaaatgttcaaagatga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcatctttgaacatttcttcagcagctgactttctagtttgttgatggatttcattatacatgcacaaaaaaagttctcgacttcgagaactttttattgtt Mask Tandem Repeat Region ================================================ aacaataaaaagttctcgaagtcgagaactttttttgtgcatgtataatgaaatccatcaacaaactagaaagtcagctgctgaagaaatgttcaaagatga Find is-nt database================================================ Query_seq: SSA_1853:SSA_1854|SSA_1853:SSA_1854:S-ribosylhomocysteine lyase, putative:Conserved uncharacterized protein:-><-:1849421..1849522 102 aacaataaaaagttctcgaagtcgagaactttttttgtgcatgtataatgaaatccatcaacaaactagaaagtcagctgctgaagaaatgttcaaagatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1853:SSA_1854|SSA_1853:SSA_1854:S-ribosylhomocysteine lyase, putative:Conserved uncharacterized protein:-><-:1849421..1849522 102 aacaataaaaagttctcgaagtcgagaactttttttgtgcatgtataatgaaatccatcaacaaactagaaagtcagctgctgaagaaatgttcaaagatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1853:SSA_1854|SSA_1853:SSA_1854:S-ribosylhomocysteine lyase, putative:Conserved uncharacterized protein:-><-:1849421..1849522 102 aacaataaaaagttctcgaagtcgagaactttttttgtgcatgtataatgaaatccatcaacaaactagaaagtcagctgctgaagaaatgttcaaagatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacaataaaaagttctcgaagtcgagaactttttttgtgcatgtataatgaaatccatcaacaaactagaaagtcagctgctgaagaaatgttcaaagatga Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 5 End: 100 .... M K S S R S R E L F L C M Y N E I H Q Q T R K S A A E E M F K D .. aacaataaaaagttctcgaagtcgagaactttttttgtgcatgtataatgaaatccatcaacaaactagaaagtcagctgctgaagaaatgttcaaagatga 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================================================ aacaataaaaagttctcgaagtcgagaactttttttgtgcatgtataatgaaatccatcaacaaactagaaagtcagctgctgaagaaatgttcaaagatga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1853:SSA_1854|SSA_1853:SSA_1854:S-ribosylhomocysteine lyase, putative:Conserved uncharacterized protein:-><-:1849421..1849522 102 aacaataaaaagttctcgaagtcgagaactttttttgtgcatgtataatgaaatccatcaacaaactagaaagtcagctgctgaagaaatgttcaaagatga Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: NC_009009_SSA_1853_SSA_1854|S-ribosylhomocysteine lyase, putative:Conserved uncharacterized protein|POSITIVE:NEGATIVE|[1849421,1849522]|102 HSP 1 e-value: 5.0E-39 bit: 161.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 aacaataaaaagttctcgaagtcgagaacnnnnnnngtgcatgtataatgaaatccatcaacaaactagaaagtcagctgctgaagaaatgttcaaagatga aacaataaaaagttctcgaagtcgagaactttttttgtgcatgtataatgaaatccatcaacaaactagaaagtcagctgctgaagaaatgttcaaagatga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAUAAAAAGUUCUCGAAGUCGAGAACUUUUUUUGUGCAUGUAUAAUGAAAUCCAUCAACAAACUAGAAAGUCAGCUGCUGAAGAAAUGUUCAAAGAUGA .((((.((((((((((((....)))))))))))))))).(((.....))).....((((....(((.......((((...))))......)))....)))). (-23.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUCUUUGAACAUUUCUUCAGCAGCUGACUUUCUAGUUUGUUGAUGGAUUUCAUUAUACAUGCACAAAAAAAGUUCUCGACUUCGAGAACUUUUUAUUGUU .......((((...(((.((((((((((......))).))))))).))).))))..........((((((((((((((((....)))))))))))).)))). (-28.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 44 7 199 162 NC_009009:SSA_0880|5end_Lipoprotein,_putative_875451..875681_POSITIVE 260 96 54 87 45 NC_009009:SSA_1424|5end_Hydrolase,_putative_1434479..1434709_NEGATIVE 253 59 12 92 29 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 245 100 68 223 189 NC_009009:SSA_1555|5end_Glucose-6-phosphate_1-dehydrogenase,_putative_1556942..1557172_POSITIVE 243 89 49 77 27 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 242 87 68 53 33 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 239 41 10 152 116 NC_009009:SSA_2033|5end_30S_ribosomal_protein_S9,_putative_2038779..2039009_NEGATIVE 222 98 63 167 133 NC_009009:SSA_1229|5end_hypothetical_protein_1252421..1252651_NEGATIVE 220 96 57 54 11 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 220 84 54 192 157 NC_009009:SSA_2158|5end_Methyltransferase,_putative_2159053..2159283_NEGATIVE 219 100 53 160 110 NC_009009:SSA_2090|5end_Hexulose-6-phosphate_synthase,_putative_2095038..2095268_NEGATIVE 219 82 49 59 22 NC_009009:SSA_1992|5end_Fructose-bisphosphate_aldolase,_putative_1989972..1990202_NEGATIVE 218 100 62 76 30 NC_009009:SSA_1396|5end_hypothetical_protein_1410374..1410604_NEGATIVE 216 79 31 69 3 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 214 59 15 181 128 NC_009009:SSA_0284|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIC_component,_putative_274888..275118_POSITIVE 210 82 54 62 33 NC_009009:SSA_2285|5end_hypothetical_protein_2287404..2287634_POSITIVE 210 98 54 204 153 NC_009009:SSA_0579|5end_Hydrolase,_HAD_superfamily,_putative_572220..572450_POSITIVE 210 82 44 155 120 NC_009009:SSA_0049|5end_Dihydroxyacetone_kinase_(Dak1),_putative_53612..53842_POSITIVE 209 88 57 227 194 NC_009009:SSA_1656|5end_Nisin_resistance_protein,_putative_1652890..1653120_NEGATIVE 209 82 59 29 1 NC_009009:SSA_1086|5end_TRNA_nucleotidyltransferase,_putative_1103328..1103558_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 38 2 89 53 NC_009009:SSA_1853|3end_S-ribosylhomocysteine_lyase,_putative_1849360..1849510_POSITIVE 264 44 7 104 67 NC_009009:SSA_0879|3end_Cell_division_regulator,_negative_regulator_of_FtsZ_septation_ring_formation,_putative_875436..875586_POSITIVE 253 59 12 95 32 NC_009009:SSA_0777|3end_Glycogen_biosynthesis_protein_GlgD,_putative_760649..760799_POSITIVE 245 100 68 48 14 NC_009009:SSA_1554|3end_hypothetical_protein_1556847..1556997_POSITIVE 239 41 10 133 97 NC_009009:SSA_2034|3end_50S_ribosomal_protein_L13,_putative_2038798..2038948_NEGATIVE 230 96 52 78 32 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE 220 84 54 139 104 NC_009009:SSA_2159|3end_hypothetical_protein_2159106..2159256_NEGATIVE 219 100 53 136 86 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 219 82 55 32 1 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 210 98 73 80 58 NC_009009:SSA_1582|3end_Esterase,_alpha/beta_hydrolase_superfamily,_putative_1585443..1585593_POSITIVE 204 78 31 151 105 NC_009009:SSA_0377|3end_ABC-type_methionine_transporter,_permease_component,_putative_367218..367368_POSITIVE 202 87 54 72 33 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 201 81 57 150 122 NC_009009:SSA_1657|3end_hypothetical_protein_1652962..1653112_NEGATIVE 200 42 1 91 55 NC_009009:SSA_1032|3end_30S_ribosomal_protein_subunit_S20,_putative_1048313..1048463_NEGATIVE 198 94 67 53 24 NC_009009:SSA_0907|3end_Fibronectin-binding_protein_A,_putative_917568..917718_NEGATIVE 197 84 47 122 84 NC_009009:SSA_2322|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327645..2327795_POSITIVE 197 84 43 143 110 NC_009009:SSA_1672|3end_hypothetical_protein_1670291..1670441_NEGATIVE 195 98 54 133 75 NC_009009:SSA_1800|3end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1781037..1781187_NEGATIVE 195 85 41 50 6 NC_009009:SSA_1577|3end_Proline_dipeptidase,_putative_1581456..1581606_POSITIVE 195 60 14 80 31 NC_009009:SSA_1484|3end_DNA_ligase,_putative_1490230..1490380_NEGATIVE