Origin IGS: taaatgagcaagaacttagaaggtcggattgacgttttgagtttttgctcttttttttacaaaaacaataggtttatgttacaaaatatttcaaacagatgaaaacatatcatttttttcaaaacttgcttacagtcgaaaataaaagactcctatgacttttttattttcacaaaaaaaggtaaaatagaatgaagtatgaatggaagaggttgctt .........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 aagcaacctcttccattcatacttcattctattttacctttttttgtgaaaataaaaaagtcataggagtcttttattttcgactgtaagcaagttttgaaaaaaatgatatgttttcatctgtttgaaatattttgtaacataaacctattgtttttgtaaaaaaaagagcaaaaactcaaaacgtcaatccgaccttctaagttcttgctcattta Mask Tandem Repeat Region ================================================ taaatgagcaagaacttagaaggtcggattgacgttttgagtttttgctcttttttttacaaaaacaataggtttatgttacaaaatatttcaaacagatgaaaacatatcatttttttcaaaacttgcttacagtcgaaaataaaagactcctatgacttttttattttcacaaaaaaaggtaaaatagaatgaagtatgaatggaagaggttgctt Find is-nt database================================================ Query_seq: SSA_0651:SSA_0652|SSA_0651:SSA_0652:hypothetical protein:UDP-N-acetylmuramoylalanine--D-glutamate ligase, putative:->->:634958..635175 218 taaatgagcaagaacttagaaggtcggattgacgttttgagtttttgctcttttttttacaaaaacaataggtttatgttacaaaatatttcaaacagatgaaaacatatcatttttttcaaaacttgcttacagtcgaaaataaaagactcctatgacttttttattttcacaaaaaaaggtaaaatagaatgaagtatgaatggaagaggttgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0651:SSA_0652|SSA_0651:SSA_0652:hypothetical protein:UDP-N-acetylmuramoylalanine--D-glutamate ligase, putative:->->:634958..635175 218 taaatgagcaagaacttagaaggtcggattgacgttttgagtttttgctcttttttttacaaaaacaataggtttatgttacaaaatatttcaaacagatgaaaacatatcatttttttcaaaacttgcttacagtcgaaaataaaagactcctatgacttttttattttcacaaaaaaaggtaaaatagaatgaagtatgaatggaagaggttgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0651:SSA_0652|SSA_0651:SSA_0652:hypothetical protein:UDP-N-acetylmuramoylalanine--D-glutamate ligase, putative:->->:634958..635175 218 taaatgagcaagaacttagaaggtcggattgacgttttgagtttttgctcttttttttacaaaaacaataggtttatgttacaaaatatttcaaacagatgaaaacatatcatttttttcaaaacttgcttacagtcgaaaataaaagactcctatgacttttttattttcacaaaaaaaggtaaaatagaatgaagtatgaatggaagaggttgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatgagcaagaacttagaaggtcggattgacgttttgagtttttgctcttttttttacaaaaacaataggtttatgttacaaaatatttcaaacagatgaaaacatatcatttttttcaaaacttgcttacagtcgaaaataaaagactcctatgacttttttattttcacaaaaaaaggtaaaatagaatgaagtatgaatggaagaggttgctt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 4 End: 99 ... M S K N L E G R I D V L S F C S F F Y K N N R F M L Q N I S N R ....................................................................................................................... taaatgagcaagaacttagaaggtcggattgacgttttgagtttttgctcttttttttacaaaaacaataggtttatgttacaaaatatttcaaacagatgaaaacatatcatttttttcaaaacttgcttacagtcgaaaataaaagactcctatgacttttttattttcacaaaaaaaggtaaaatagaatgaagtatgaatggaagaggttgctt 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================================================ taaatgagcaagaacttagaaggtcggattgacgttttgagtttttgctcttttttttacaaaaacaataggtttatgttacaaaatatttcaaacagatgaaaacatatcatttttttcaaaacttgcttacagtcgaaaataaaagactcctatgacttttttattttcacaaaaaaaggtaaaatagaatgaagtatgaatggaagaggttgctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0651:SSA_0652|SSA_0651:SSA_0652:hypothetical protein:UDP-N-acetylmuramoylalanine--D-glutamate ligase, putative:->->:634958..635175 218 taaatgagcaagaacttagaaggtcggattgacgttttgagtttttgctcttttttttacaaaaacaataggtttatgttacaaaatatttcaaacagatgaaaacatatcatttttttcaaaacttgcttacagtcgaaaataaaagactcctatgacttttttattttcacaaaaaaaggtaaaatagaatgaagtatgaatggaagaggttgctt Intra-Species Hit: Count: 1 Min: 1 Max: 218 Len: 218 Subject: NC_009009_SSA_0651_SSA_0652|hypothetical protein:UDP-N-acetylmuramoylalanine--D-glutamate ligase, putative|POSITIVE:POSITIVE|[634958,635175]|218 HSP 1 e-value: 5.0E-81 bit: 301.0 Len: 218 Query Start:1 Query End:218 Subject Strand: POSITIVE Subject Start: 1 Subject End: 218 taaatgagcaagaacttagaaggtcggattgacgttttgagtttttgctcnnnnnnnnacaaaaacaataggtttatgttacaaaatatttcaaacagatgaaaacatatcannnnnnncaaaacttgcttacagtcgaaaataaaagactcctatgacttttttattttcacnnnnnnnggtaaaatagaatgaagtatgaatggaagaggttgctt taaatgagcaagaacttagaaggtcggattgacgttttgagtttttgctcttttttttacaaaaacaataggtttatgttacaaaatatttcaaacagatgaaaacatatcatttttttcaaaacttgcttacagtcgaaaataaaagactcctatgacttttttattttcacaaaaaaaggtaaaatagaatgaagtatgaatggaagaggttgctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUGAGCAAGAACUUAGAAGGUCGGAUUGACGUUUUGAGUUUUUGCUCUUUUUUUUACAAAAACAAUAGGUUUAUGUUACAAAAUAUUUCAAACAGAUGAAAACAUAUCAUUUUUUUCAAAACUUGCUUACAGUCGAAAAUAAAAGACUCCUAUGACUUUUUUAUUUUCACAAAAAAAGGUAAAAUAGAAUGAAGUAUGAAUGGAAGAGGUUGCUU .....((((((((((((((((.(((.....))).))))))))))))))))...............((((...(((((..(((......(((((......))))).....(((((((.......((((.......((.((((((((((((.((....)).))))))))))))))......)))).....))))))).)))...)))))....))))... (-48.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCAACCUCUUCCAUUCAUACUUCAUUCUAUUUUACCUUUUUUUGUGAAAAUAAAAAAGUCAUAGGAGUCUUUUAUUUUCGACUGUAAGCAAGUUUUGAAAAAAAUGAUAUGUUUUCAUCUGUUUGAAAUAUUUUGUAACAUAAACCUAUUGUUUUUGUAAAAAAAAGAGCAAAAACUCAAAACGUCAAUCCGACCUUCUAAGUUCUUGCUCAUUUA ......................................((((((((..(((((((...((((...((((........))))))))....((((((((..((....((((.......))))...))..))))...))))............)))))))..)))))))).((((((.((((......(((.....)))......)))).))))))..... (-34.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 56 12 195 139 NC_009009:SSA_1144|5end_Beta-N-acetylhexosaminidase,_putative_1175610..1175840_NEGATIVE 268 61 22 117 81 NC_009009:SSA_1769|5end_hypothetical_protein_1757490..1757720_NEGATIVE 268 51 18 145 107 NC_009009:SSA_0392|5end_hypothetical_protein_387876..388106_POSITIVE 256 49 5 65 20 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 256 70 21 116 58 NC_009009:SSA_0378|5end_TRZ/ATZ_family_hydrolase,_putative_367276..367506_POSITIVE 252 47 6 166 129 NC_009009:SSA_1444|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1447267..1447497_NEGATIVE 248 47 3 220 184 NC_009009:SSA_0613|5end_Glucosyltransferase,_putative_601847..602077_POSITIVE 245 50 17 217 186 NC_009009:SSA_1078|5end_hypothetical_protein_1095742..1095972_POSITIVE 243 67 21 171 126 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 243 154 116 129 85 NC_009009:SSA_0755|5end_hypothetical_protein_736212..736442_POSITIVE 237 52 16 66 33 NC_009009:SSA_1220|5end_DNA_gyrase_A_subunit,_putative_1243832..1244062_NEGATIVE 234 50 7 231 196 NC_009009:SSA_1754|5end_hypothetical_protein_1743478..1743708_NEGATIVE 233 84 42 142 97 NC_009009:SSA_0847|5end_6-phosphofructokinase,_putative_833372..833602_POSITIVE 230 180 134 167 132 NC_009009:SSA_2032|5end_Integrase/recombinase,_phage_integrase_family,_putative_2038006..2038236_POSITIVE 230 47 7 71 25 NC_009009:SSA_1480|5end_hypothetical_protein_1484811..1485041_NEGATIVE 227 42 5 123 85 NC_009009:SSA_0819|5end_hypothetical_protein_800418..800648_POSITIVE 226 207 165 205 152 NC_009009:SSA_1385|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_1402268..1402498_POSITIVE 226 56 19 98 64 NC_009009:SSA_0093|5end_V-type_sodium_ATPase,_subunit_D,_putative_94286..94516_POSITIVE 224 50 3 67 8 NC_009009:SSA_2004|5end_Zinc_metalloprotease_zmpB_precursor,_putative_2004930..2005160_NEGATIVE 224 177 135 127 87 NC_009009:SSA_0751|5end_Oligoendopeptidase_F,_putative_732367..732597_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 50 6 85 41 NC_009009:SSA_0651|3end_hypothetical_protein_634897..635047_POSITIVE 273 56 12 111 55 NC_009009:SSA_1145|3end_hypothetical_protein_1175694..1175844_NEGATIVE 268 61 22 123 87 NC_009009:SSA_1770|3end_hypothetical_protein_1757484..1757634_NEGATIVE 252 47 6 131 94 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 248 47 3 150 114 NC_009009:SSA_0612|3end_Rgg_protein,_putative_601857..602007_POSITIVE 238 54 16 92 60 NC_009009:SSA_1027|3end_hypothetical_protein_1045244..1045394_POSITIVE 233 57 18 75 40 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 233 84 42 57 12 NC_009009:SSA_0846|3end_DNA-polymerase_III_alpha-chain,_putative_833367..833517_POSITIVE 230 47 7 56 10 NC_009009:SSA_1481|3end_FmtA-like_protein,_putative_1484826..1484976_NEGATIVE 227 42 5 111 73 NC_009009:SSA_0818|3end_SPX_domain-like_protein,_putative_800486..800636_POSITIVE 226 56 19 101 67 NC_009009:SSA_0092|3end_V-type_sodium_ATPase,_subunit_B,_putative_94369..94519_POSITIVE 223 61 21 72 36 NC_009009:SSA_1953|3end_NifU_family_protein,_putative_1949642..1949792_NEGATIVE 223 49 1 56 13 NC_009009:SSA_1028|3end_Transcriptional_repressor,_XRE_family,_putative_1045290..1045440_NEGATIVE 221 47 9 75 40 NC_009009:SSA_2204|3end_hypothetical_protein_2205507..2205657_POSITIVE 221 60 14 59 6 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 221 36 5 28 1 NC_009009:SSA_1292|3end_hypothetical_protein_1311099..1311249_NEGATIVE 220 167 126 70 27 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 217 44 5 86 31 NC_009009:SSA_2081|3end_hypothetical_protein_2085490..2085640_POSITIVE 217 41 7 149 113 NC_009009:SSA_1138|3end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1166884..1167034_POSITIVE 216 53 11 77 38 NC_009009:SSA_0062|3end_Aldose_1-epimerase,_putative_64858..65008_POSITIVE