Origin IGS: cctctctaaaaacgaatcgtatttttcggactctctctggtgacagggagagttttctttatatcaaaactttcccttgccattctgctggaagtctgctataatagttatttgtgagcaaacctcacttaccccttgcaaagtcttggggtcattagaccaaaaggaggaaaaatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgatttttcctccttttggtctaatgaccccaagactttgcaaggggtaagtgaggtttgctcacaaataactattatagcagacttccagcagaatggcaagggaaagttttgatataaagaaaactctccctgtcaccagagagagtccgaaaaatacgattcgtttttagagagg Mask Tandem Repeat Region ================================================ cctctctaaaaacgaatcgtatttttcggactctctctggtgacagggagagttttctttatatcaaaactttcccttgccattctgctggaagtctgctataatagttatttgtgagcaaacctcacttaccccttgcaaagtcttggggtcattagaccaaaaggaggaaaaatca Find is-nt database================================================ Query_seq: SSA_0436:SSA_0437|SSA_0436:SSA_0437:Imidazolonepropionase, putative:30S ribosomal protein S6, putative:->->:440275..440452 178 cctctctaaaaacgaatcgtatttttcggactctctctggtgacagggagagttttctttatatcaaaactttcccttgccattctgctggaagtctgctataatagttatttgtgagcaaacctcacttaccccttgcaaagtcttggggtcattagaccaaaaggaggaaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0436:SSA_0437|SSA_0436:SSA_0437:Imidazolonepropionase, putative:30S ribosomal protein S6, putative:->->:440275..440452 178 cctctctaaaaacgaatcgtatttttcggactctctctggtgacagggagagttttctttatatcaaaactttcccttgccattctgctggaagtctgctataatagttatttgtgagcaaacctcacttaccccttgcaaagtcttggggtcattagaccaaaaggaggaaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0436:SSA_0437|SSA_0436:SSA_0437:Imidazolonepropionase, putative:30S ribosomal protein S6, putative:->->:440275..440452 178 cctctctaaaaacgaatcgtatttttcggactctctctggtgacagggagagttttctttatatcaaaactttcccttgccattctgctggaagtctgctataatagttatttgtgagcaaacctcacttaccccttgcaaagtcttggggtcattagaccaaaaggaggaaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctctctaaaaacgaatcgtatttttcggactctctctggtgacagggagagttttctttatatcaaaactttcccttgccattctgctggaagtctgctataatagttatttgtgagcaaacctcacttaccccttgcaaagtcttggggtcattagaccaaaaggaggaaaaatca Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 16 End: 114 ............... M V F F G L S L V T G R V F F I S K L S L A I L L E V C Y N S Y L ................................................................ Protein_Len: 34 Strand: + Start: 77 End: 178 ............................................................................ M P F C W K S A I I V I C E Q T S L T P C K V L G S L D Q K E E K S cctctctaaaaacgaatcgtatttttcggactctctctggtgacagggagagttttctttatatcaaaactttcccttgccattctgctggaagtctgctataatagttatttgtgagcaaacctcacttaccccttgcaaagtcttggggtcattagaccaaaaggaggaaaaatca 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: 89 Start: 76 End: 105 ...........................................................................CTTGCCATTCTGCTGGAAGTCTGCTATAAT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cctctctaaaaacgaatcgtatttttcggactctctctggtgacagggagagttttctttatatcaaaactttcccttgccattctgctggaagtctgctataatagttatttgtgagcaaacctcacttaccccttgcaaagtcttggggtcattagaccaaaaggaggaaaaatca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -3.2 Tail_Score: -3.41229 Start: 41 End: 82 Full_Region: TCGGACTCTCTCTGG TGACAGGGAGAGTTTT CTTTATATC AAAACTTTCCCTTGCCA TTCTGCTGGAAGTCT ........................................TGACAGGGAGAGTTTTCTTTATATCAAAACTTTCCCTTGCCA................................................................................................ Find igs database================================================ Query_seq: SSA_0436:SSA_0437|SSA_0436:SSA_0437:Imidazolonepropionase, putative:30S ribosomal protein S6, putative:->->:440275..440452 178 cctctctaaaaacgaatcgtatttttcggactctctctggtgacagggagagttttctttatatcaaaactttcccttgccattctgctggaagtctgctataatagttatttgtgagcaaacctcacttaccccttgcaaagtcttggggtcattagaccaaaaggaggaaaaatca Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: NC_009009_SSA_0436_SSA_0437|Imidazolonepropionase, putative:30S ribosomal protein S6, putative|POSITIVE:POSITIVE|[440275,440452]|178 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 cctctctaaaaacgaatcgtatttttcggactctctctggtgacagggagagttttctttatatcaaaactttcccttgccattctgctggaagtctgctataatagttatttgtgagcaaacctcacttaccccttgcaaagtcttggggtcattagaccaaaaggaggaaaaatca cctctctaaaaacgaatcgtatttttcggactctctctggtgacagggagagttttctttatatcaaaactttcccttgccattctgctggaagtctgctataatagttatttgtgagcaaacctcacttaccccttgcaaagtcttggggtcattagaccaaaaggaggaaaaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCUCUAAAAACGAAUCGUAUUUUUCGGACUCUCUCUGGUGACAGGGAGAGUUUUCUUUAUAUCAAAACUUUCCCUUGCCAUUCUGCUGGAAGUCUGCUAUAAUAGUUAUUUGUGAGCAAACCUCACUUACCCCUUGCAAAGUCUUGGGGUCAUUAGACCAAAAGGAGGAAAAAUCA ..................(.(((((((.(((((((((((....)))))))))))((((((...........((((...((......)).))))(((((...............(((((.....)))))..(((((..(......)..)))))...)))))..)))))).)))))))). (-47.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUUUCCUCCUUUUGGUCUAAUGACCCCAAGACUUUGCAAGGGGUAAGUGAGGUUUGCUCACAAAUAACUAUUAUAGCAGACUUCCAGCAGAAUGGCAAGGGAAAGUUUUGAUAUAAAGAAAACUCUCCCUGUCACCAGAGAGAGUCCGAAAAAUACGAUUCGUUUUUAGAGAGG ..((((((((((.(((((((((....(((((............)))))..(.((((((((((................)))))))))))...)))..((((.((((.((((((.........)))))).)))))))).)))))).)))...))))))).................... (-45.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 160 114 58 14 NC_009009:SSA_0652|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase,_putative_635036..635266_POSITIVE 320 150 110 57 14 NC_009009:SSA_1303|5end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322992..1323222_NEGATIVE 316 99 70 89 55 NC_009009:SSA_0471|5end_CbiG_protein,_putative_473600..473830_POSITIVE 296 116 79 62 19 NC_009009:SSA_2045|5end_Reductase,_putative_2048948..2049178_NEGATIVE 294 167 127 208 168 NC_009009:SSA_0721|5end_Mn/Fe-dependent_superoxide_dismutase,_putative_706215..706445_POSITIVE 289 98 51 143 95 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 289 50 1 39 1 NC_009009:SSA_1126|5end_Thiamine_biosynthesis_lipoprotein,_putative_1151522..1151752_NEGATIVE 283 99 71 126 97 NC_009009:SSA_2224|5end_Phosphotyrosine-protein_phosphatase,_putative_2225442..2225672_NEGATIVE 279 110 70 168 127 NC_009009:SSA_2227|5end_Acetyl_transferase,_putative_2228261..2228491_NEGATIVE 278 106 66 138 93 NC_009009:SSA_2267|5end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2266127..2266357_POSITIVE 274 118 76 73 25 NC_009009:SSA_1449|5end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1451931..1452161_NEGATIVE 274 108 63 53 15 NC_009009:SSA_0691|5end_D-ala,D-ala_ligase,_putative_675233..675463_POSITIVE 272 82 46 211 176 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 272 96 52 120 78 NC_009009:SSA_1321|5end_Ferrochelatase,_putative_1338343..1338573_NEGATIVE 268 136 94 113 69 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 267 102 63 217 189 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 265 129 85 92 46 NC_009009:SSA_0860|5end_N-acetylmuramidase/lysin,_putative_847615..847845_POSITIVE 264 170 122 154 101 NC_009009:SSA_2333|5end_Integral_membrane_protein,_putative_2336460..2336690_NEGATIVE 264 96 51 205 154 NC_009009:SSA_1267|5end_crcB-like_protein_2,_putative_1291347..1291577_NEGATIVE 264 78 32 188 143 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 166 123 143 90 NC_009009:SSA_1803|3end_GTP-binding_protein,_putative_1786599..1786749_NEGATIVE 316 99 70 141 107 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 303 119 75 135 95 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 296 116 79 53 10 NC_009009:SSA_2046|3end_Uridine_phosphorylase,_putative_2048957..2049107_NEGATIVE 294 103 70 39 1 NC_009009:SSA_1843|3end_Histidine_kinase,_putative_1836472..1836622_NEGATIVE 294 167 127 145 105 NC_009009:SSA_0720|3end_hypothetical_protein_706232..706382_POSITIVE 289 98 51 141 93 NC_009009:SSA_1403|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1416222..1416372_NEGATIVE 283 99 71 129 100 NC_009009:SSA_2225|3end_Transcriptional_attenuator_LytR,_putative_2225439..2225589_NEGATIVE 281 168 122 65 17 NC_009009:SSA_0081|3end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_84220..84370_NEGATIVE 280 79 35 68 16 NC_009009:SSA_1166|3end_hypothetical_protein_1192350..1192500_POSITIVE 278 99 57 109 72 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 277 159 126 66 31 NC_009009:SSA_1387|3end_hypothetical_protein_1403497..1403647_NEGATIVE 271 77 38 46 9 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 265 161 124 83 36 NC_009009:SSA_1711|3end_Endonuclease_III,_putative_1699007..1699157_NEGATIVE 264 78 32 80 35 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 260 100 51 143 81 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 260 114 74 101 50 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 260 170 135 140 102 NC_009009:SSA_0390|3end_hypothetical_protein_385714..385864_POSITIVE 259 170 123 120 82 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 259 100 70 67 28 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE