Origin IGS: aaaaatgttgaaaaaagacttgtcctcccaaaggtgacaagttttttaaaagttggagagaaaagttgaaatcgaaagaattagtttatttagcgagtacggctattttgttggcagcgactgccaatgttgcaaaagccgaggaacatactgtcgctgagtcaggagttttaaaaacagaaaggtctgttagttcccagaatcagaca .........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 tgtctgattctgggaactaacagacctttctgtttttaaaactcctgactcagcgacagtatgttcctcggcttttgcaacattggcagtcgctgccaacaaaatagccgtactcgctaaataaactaattctttcgatttcaacttttctctccaacttttaaaaaacttgtcacctttgggaggacaagtcttttttcaacattttt Mask Tandem Repeat Region ================================================ aaaaatgttgaaaaaagacttgtcctcccaaaggtgacaagttttttaaaagttggagagaaaagttgaaatcgaaagaattagtttatttagcgagtacggctattttgttggcagcgactgccaatgttgcaaaagccgaggaacatactgtcgctgagtcaggagttttaaaaacagaaaggtctgttagttcccagaatcagaca Find is-nt database================================================ Query_seq: SSA_0859:SSA_0860|SSA_0859:SSA_0860:Triosephosphate isomerase, putative:N-acetylmuramidase/lysin, putative:->->:847546..847754 209 aaaaatgttgaaaaaagacttgtcctcccaaaggtgacaagttttttaaaagttggagagaaaagttgaaatcgaaagaattagtttatttagcgagtacggctattttgttggcagcgactgccaatgttgcaaaagccgaggaacatactgtcgctgagtcaggagttttaaaaacagaaaggtctgttagttcccagaatcagaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0859:SSA_0860|SSA_0859:SSA_0860:Triosephosphate isomerase, putative:N-acetylmuramidase/lysin, putative:->->:847546..847754 209 aaaaatgttgaaaaaagacttgtcctcccaaaggtgacaagttttttaaaagttggagagaaaagttgaaatcgaaagaattagtttatttagcgagtacggctattttgttggcagcgactgccaatgttgcaaaagccgaggaacatactgtcgctgagtcaggagttttaaaaacagaaaggtctgttagttcccagaatcagaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0859:SSA_0860|SSA_0859:SSA_0860:Triosephosphate isomerase, putative:N-acetylmuramidase/lysin, putative:->->:847546..847754 209 aaaaatgttgaaaaaagacttgtcctcccaaaggtgacaagttttttaaaagttggagagaaaagttgaaatcgaaagaattagtttatttagcgagtacggctattttgttggcagcgactgccaatgttgcaaaagccgaggaacatactgtcgctgagtcaggagttttaaaaacagaaaggtctgttagttcccagaatcagaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaatgttgaaaaaagacttgtcctcccaaaggtgacaagttttttaaaagttggagagaaaagttgaaatcgaaagaattagtttatttagcgagtacggctattttgttggcagcgactgccaatgttgcaaaagccgaggaacatactgtcgctgagtcaggagttttaaaaacagaaaggtctgttagttcccagaatcagaca Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 53 End: 157 .................................................... M E R K V E I E R I S L F S E Y G Y F V G S D C Q C C K S R G T Y C R .................................................... Protein_Len: 48 Strand: + Start: 66 End: 209 ................................................................. M K S K E L V Y L A S T A I L L A A T A N V A K A E E H T V A E S G V L K T E R S V S S Q N Q T aaaaatgttgaaaaaagacttgtcctcccaaaggtgacaagttttttaaaagttggagagaaaagttgaaatcgaaagaattagtttatttagcgagtacggctattttgttggcagcgactgccaatgttgcaaaagccgaggaacatactgtcgctgagtcaggagttttaaaaacagaaaggtctgttagttcccagaatcagaca 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================================================ aaaaatgttgaaaaaagacttgtcctcccaaaggtgacaagttttttaaaagttggagagaaaagttgaaatcgaaagaattagtttatttagcgagtacggctattttgttggcagcgactgccaatgttgcaaaagccgaggaacatactgtcgctgagtcaggagttttaaaaacagaaaggtctgttagttcccagaatcagaca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 79 HP_score: -10.9 Tail_Score: -3.01712 Start: 111 End: 127 Full_Region: AGTACGGCTATTTTG TTGGCAG CGA CTGCCAA TGTTGCAAAAGCCGA ..............................................................................................................TTGGCAGCGACTGCCAA.................................................................................. Find igs database================================================ Query_seq: SSA_0859:SSA_0860|SSA_0859:SSA_0860:Triosephosphate isomerase, putative:N-acetylmuramidase/lysin, putative:->->:847546..847754 209 aaaaatgttgaaaaaagacttgtcctcccaaaggtgacaagttttttaaaagttggagagaaaagttgaaatcgaaagaattagtttatttagcgagtacggctattttgttggcagcgactgccaatgttgcaaaagccgaggaacatactgtcgctgagtcaggagttttaaaaacagaaaggtctgttagttcccagaatcagaca Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: NC_009009_SSA_0859_SSA_0860|Triosephosphate isomerase, putative:N-acetylmuramidase/lysin, putative|POSITIVE:POSITIVE|[847546,847754]|209 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 aaaaatgttgaaaaaagacttgtcctcccaaaggtgacaagttttttaaaagttggagagaaaagttgaaatcgaaagaattagtttatttagcgagtacggctattttgttggcagcgactgccaatgttgcaaaagccgaggaacatactgtcgctgagtcaggagttttaaaaacagaaaggtctgttagttcccagaatcagaca aaaaatgttgaaaaaagacttgtcctcccaaaggtgacaagttttttaaaagttggagagaaaagttgaaatcgaaagaattagtttatttagcgagtacggctattttgttggcagcgactgccaatgttgcaaaagccgaggaacatactgtcgctgagtcaggagttttaaaaacagaaaggtctgttagttcccagaatcagaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUGUUGAAAAAAGACUUGUCCUCCCAAAGGUGACAAGUUUUUUAAAAGUUGGAGAGAAAAGUUGAAAUCGAAAGAAUUAGUUUAUUUAGCGAGUACGGCUAUUUUGUUGGCAGCGACUGCCAAUGUUGCAAAAGCCGAGGAACAUACUGUCGCUGAGUCAGGAGUUUUAAAAACAGAAAGGUCUGUUAGUUCCCAGAAUCAGACA .....((((((.((((((((((((..((....)).)))))))))))).....((((.(((.....((((..((....))..........(((((((...(((((..(((((((((((...)))))).....)))))))))).((......)).))))))).))))..........((((((....))))))..)))))))..))).))) (-54.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCUGAUUCUGGGAACUAACAGACCUUUCUGUUUUUAAAACUCCUGACUCAGCGACAGUAUGUUCCUCGGCUUUUGCAACAUUGGCAGUCGCUGCCAACAAAAUAGCCGUACUCGCUAAAUAAACUAAUUCUUUCGAUUUCAACUUUUCUCUCCAACUUUUAAAAAACUUGUCACCUUUGGGAGGACAAGUCUUUUUUCAACAUUUUU .(.((((.((.((((...((((((....))))))........)))))).)))))...(((..((....(((((((((.....(((((((...)))))))))))..))))).))..)))............................................((((.(((((((.((....))..))))))).))))............ (-42.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 140 91 89 34 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 365 160 113 192 139 NC_009009:SSA_0592|5end_hypothetical_protein_583626..583856_POSITIVE 345 170 121 211 151 NC_009009:SSA_1441|5end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1445183..1445413_NEGATIVE 342 133 92 67 8 NC_009009:SSA_1154|5end_hypothetical_protein_1182661..1182891_POSITIVE 339 158 111 50 3 NC_009009:SSA_0941|5end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_949157..949387_POSITIVE 337 140 91 75 32 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 329 155 112 74 34 NC_009009:SSA_1485|5end_Citrulline_cluster-linked_gene,_putative_1492809..1493039_NEGATIVE 327 159 111 65 14 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 326 140 93 69 17 NC_009009:SSA_1950|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component,_putative_1946527..1946757_NEGATIVE 325 159 111 75 19 NC_009009:SSA_1044|5end_Homoserine_kinase,_putative_1059853..1060083_POSITIVE 316 159 112 209 159 NC_009009:SSA_0106|5end_30S_ribosomal_protein_S10,_putative_107772..108002_POSITIVE 314 159 114 79 31 NC_009009:SSA_1267|5end_crcB-like_protein_2,_putative_1291347..1291577_NEGATIVE 313 143 113 62 32 NC_009009:SSA_0478|5end_Cobalt_transport_protein_cbiN,_putative_480002..480232_POSITIVE 313 158 113 59 14 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 311 169 129 208 170 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 310 140 91 204 154 NC_009009:SSA_2125|5end_Small_primase-like_protein_(Toprim_domain),_putative_2130019..2130249_NEGATIVE 310 133 92 49 7 NC_009009:SSA_1038|5end_Lipoprotein,_putative_1052579..1052809_POSITIVE 310 159 114 60 1 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 306 140 91 223 162 NC_009009:SSA_1393|5end_hypothetical_protein_1408773..1409003_NEGATIVE 305 160 115 183 134 NC_009009:SSA_0152|5end_hypothetical_protein_145799..146029_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 140 91 63 8 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 342 133 92 74 15 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 342 160 112 79 8 NC_009009:SSA_1012|3end_Phosphoenolpyruvate_synthase,_putative_1017314..1017464_POSITIVE 341 158 116 70 23 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 331 200 156 77 28 NC_009009:SSA_1530|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1537510..1537660_NEGATIVE 327 159 111 72 21 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 327 125 90 149 110 NC_009009:SSA_0378|3end_TRZ/ATZ_family_hydrolase,_putative_368627..368777_POSITIVE 325 159 111 73 17 NC_009009:SSA_1043|3end_Homoserine_dehydrogenase,_putative_1059931..1060081_POSITIVE 316 160 112 131 96 NC_009009:SSA_0540|3end_Glycerol_uptake_facilitator_protein,_putative_535748..535898_POSITIVE 314 159 114 79 31 NC_009009:SSA_1268|3end_Chorismate_mutase/prephenate_dehydratase,_putative_1291347..1291497_NEGATIVE 313 143 113 65 35 NC_009009:SSA_0477|3end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_480085..480235_POSITIVE 313 158 113 49 4 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 309 140 91 148 80 NC_009009:SSA_1053|3end_Pyruvate_phosphate_dikinase,_putative_1067447..1067597_NEGATIVE 302 169 121 138 91 NC_009009:SSA_0390|3end_hypothetical_protein_385714..385864_POSITIVE 300 140 92 74 9 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 297 140 96 71 17 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 297 200 151 79 18 NC_009009:SSA_0586|3end_Conserved_uncharacterized_protein_578243..578393_POSITIVE 295 133 93 45 5 NC_009009:SSA_2297|3end_hypothetical_protein_2298776..2298926_NEGATIVE 291 156 112 146 108 NC_009009:SSA_1866|3end_hypothetical_protein_1861958..1862108_NEGATIVE 290 160 111 82 33 NC_009009:SSA_1083|3end_Conserved_uncharacterized_protein_1101752..1101902_POSITIVE