Origin IGS: tagataacatccgccacaatgtggtggatttttttgactcattgtcaattatagtagggaatttatggcgaaggaattcaagctgtttttttatgagcaatatgacaatataatccttttataagatagatttaagaaaaattttaactttttcttaaccatttttaatcttaggagattatactaaagtcataaaaaaacaaacctaaaggagaatctt .........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 aagattctcctttaggtttgtttttttatgactttagtataatctcctaagattaaaaatggttaagaaaaagttaaaatttttcttaaatctatcttataaaaggattatattgtcatattgctcataaaaaaacagcttgaattccttcgccataaattccctactataattgacaatgagtcaaaaaaatccaccacattgtggcggatgttatcta Mask Tandem Repeat Region ================================================ tagataacatccgccacaatgtggtggatttttttgactcattgtcaattatagtagggaatttatggcgaaggaattcaagctgtttttttatgagcaatatgacaatataatccttttataagatagatttaagaaaaattttaactttttcttaaccatttttaatcttaggagattatactaaagtcataaaaaaacaaacctaaaggagaatctt Find is-nt database================================================ Query_seq: SSA_1111:SSA_1112|SSA_1111:SSA_1112:Branched-chain amino acid transport system II carrier protein, putative:Cell wall surface anchor family protein, putative:->->:1138001..1138220 220 tagataacatccgccacaatgtggtggatttttttgactcattgtcaattatagtagggaatttatggcgaaggaattcaagctgtttttttatgagcaatatgacaatataatccttttataagatagatttaagaaaaattttaactttttcttaaccatttttaatcttaggagattatactaaagtcataaaaaaacaaacctaaaggagaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1111:SSA_1112|SSA_1111:SSA_1112:Branched-chain amino acid transport system II carrier protein, putative:Cell wall surface anchor family protein, putative:->->:1138001..1138220 220 tagataacatccgccacaatgtggtggatttttttgactcattgtcaattatagtagggaatttatggcgaaggaattcaagctgtttttttatgagcaatatgacaatataatccttttataagatagatttaagaaaaattttaactttttcttaaccatttttaatcttaggagattatactaaagtcataaaaaaacaaacctaaaggagaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1111:SSA_1112|SSA_1111:SSA_1112:Branched-chain amino acid transport system II carrier protein, putative:Cell wall surface anchor family protein, putative:->->:1138001..1138220 220 tagataacatccgccacaatgtggtggatttttttgactcattgtcaattatagtagggaatttatggcgaaggaattcaagctgtttttttatgagcaatatgacaatataatccttttataagatagatttaagaaaaattttaactttttcttaaccatttttaatcttaggagattatactaaagtcataaaaaaacaaacctaaaggagaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagataacatccgccacaatgtggtggatttttttgactcattgtcaattatagtagggaatttatggcgaaggaattcaagctgtttttttatgagcaatatgacaatataatccttttataagatagatttaagaaaaattttaactttttcttaaccatttttaatcttaggagattatactaaagtcataaaaaaacaaacctaaaggagaatctt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 9 End: 110 ........ M R H N V V D F F D S L S I I V G N L W R R N S S C F F M S N M T I .............................................................................................................. Protein_Len: 36 Strand: - Start: 2 End: 109 . S L M R W L T T S K K S E N D I I T P F K H R L F E L Q K K I L L I V M ............................................................................................................... tagataacatccgccacaatgtggtggatttttttgactcattgtcaattatagtagggaatttatggcgaaggaattcaagctgtttttttatgagcaatatgacaatataatccttttataagatagatttaagaaaaattttaactttttcttaaccatttttaatcttaggagattatactaaagtcataaaaaaacaaacctaaaggagaatctt 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================================================ tagataacatccgccacaatgtggtggatttttttgactcattgtcaattatagtagggaatttatggcgaaggaattcaagctgtttttttatgagcaatatgacaatataatccttttataagatagatttaagaaaaattttaactttttcttaaccatttttaatcttaggagattatactaaagtcataaaaaaacaaacctaaaggagaatctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1111:SSA_1112|SSA_1111:SSA_1112:Branched-chain amino acid transport system II carrier protein, putative:Cell wall surface anchor family protein, putative:->->:1138001..1138220 220 tagataacatccgccacaatgtggtggatttttttgactcattgtcaattatagtagggaatttatggcgaaggaattcaagctgtttttttatgagcaatatgacaatataatccttttataagatagatttaagaaaaattttaactttttcttaaccatttttaatcttaggagattatactaaagtcataaaaaaacaaacctaaaggagaatctt Intra-Species Hit: Count: 1 Min: 1 Max: 220 Len: 220 Subject: NC_009009_SSA_1111_SSA_1112|Branched-chain amino acid transport system II carrier protein, putative:Cell wall surface anchor family protein, putative|POSITIVE:POSITIVE|[1138001,1138220]|220 HSP 1 e-value: 5.0E-84 bit: 311.0 Len: 220 Query Start:1 Query End:220 Subject Strand: POSITIVE Subject Start: 1 Subject End: 220 tagataacatccgccacaatgtggtggannnnnnngactcattgtcaattatagtagggaatttatggcgaaggaattcaagctgnnnnnnnatgagcaatatgacaatataatccttttataagatagatttaagaaaaattttaactttttcttaaccatttttaatcttaggagattatactaaagtcatnnnnnnncaaacctaaaggagaatctt tagataacatccgccacaatgtggtggatttttttgactcattgtcaattatagtagggaatttatggcgaaggaattcaagctgtttttttatgagcaatatgacaatataatccttttataagatagatttaagaaaaattttaactttttcttaaccatttttaatcttaggagattatactaaagtcataaaaaaacaaacctaaaggagaatctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUAACAUCCGCCACAAUGUGGUGGAUUUUUUUGACUCAUUGUCAAUUAUAGUAGGGAAUUUAUGGCGAAGGAAUUCAAGCUGUUUUUUUAUGAGCAAUAUGACAAUAUAAUCCUUUUAUAAGAUAGAUUUAAGAAAAAUUUUAACUUUUUCUUAACCAUUUUUAAUCUUAGGAGAUUAUACUAAAGUCAUAAAAAAACAAACCUAAAGGAGAAUCUU .((((...(((((((((...)))))))))....(((((.....)))))......((((((((((.........))))))....(((((((((((((.(.....)....(((((((((....((((((((((((((((((((.......))))))))))..))))...)))))))).)))))))......)))))))))))))..)))).......)))). (-47.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUUCUCCUUUAGGUUUGUUUUUUUAUGACUUUAGUAUAAUCUCCUAAGAUUAAAAAUGGUUAAGAAAAAGUUAAAAUUUUUCUUAAAUCUAUCUUAUAAAAGGAUUAUAUUGUCAUAUUGCUCAUAAAAAAACAGCUUGAAUUCCUUCGCCAUAAAUUCCCUACUAUAAUUGACAAUGAGUCAAAAAAAUCCACCACAUUGUGGCGGAUGUUAUCUA .((((.....((((((((.(((((((((((((..(((((((((((..((((((.........((((((((((.......))))))))))....)))))).....))))))))))).......).))))))))))))))))))))....((((((((((..............(((((.....)))))..............))))))))))....)))). (-50.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 39 8 47 19 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 267 130 81 113 69 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 266 47 11 202 172 NC_009009:SSA_1935|5end_Beta-ketoacyl-ACP_synthase_II_(3-oxoacyl-(Acyl-carrier-protein)_synthase_II),_putative_1923039..1923269_NEGATIVE 260 67 27 135 93 NC_009009:SSA_1582|5end_Esterase,_alpha/beta_hydrolase_superfamily,_putative_1584671..1584901_POSITIVE 259 45 11 208 175 NC_009009:SSA_0423|5end_hypothetical_protein_421347..421577_NEGATIVE 258 45 11 63 27 NC_009009:SSA_0907|5end_Fibronectin-binding_protein_A,_putative_919217..919447_NEGATIVE 257 88 44 102 53 NC_009009:SSA_1579|5end_ABC-type_Fe3+-siderophore_transport_system,_ATPase_component,_putative_1582851..1583081_POSITIVE 252 178 138 208 170 NC_009009:SSA_1759|5end_hypothetical_protein_1746969..1747199_NEGATIVE 252 47 9 97 54 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 245 58 11 196 145 NC_009009:SSA_2226|5end_Organic_radical_activating_chaperone,_putative_2227756..2227986_NEGATIVE 244 46 3 95 50 NC_009009:SSA_0092|5end_V-type_sodium_ATPase,_subunit_B,_putative_92895..93125_POSITIVE 242 39 11 30 6 NC_009009:SSA_2162|5end_hypothetical_protein_2160592..2160822_POSITIVE 241 75 31 64 16 NC_009009:SSA_1386|5end_NADPH-dependent_FMN_reductase,_putative_1402800..1403030_POSITIVE 239 62 23 216 162 NC_009009:SSA_0390|5end_hypothetical_protein_385002..385232_POSITIVE 236 58 13 97 38 NC_009009:SSA_0257|5end_N-acetylmuramidase/lysin,_putative_248878..249108_POSITIVE 234 69 22 118 71 NC_009009:SSA_1297|5end_Nuclease_subunit_of_the_excinuclease_complex,_subunit_C,_putative_1314976..1315206_NEGATIVE 231 59 12 98 50 NC_009009:SSA_2191|5end_Conserved_uncharacterized_protein_2192049..2192279_POSITIVE 231 90 49 76 42 NC_009009:SSA_1257|5end_hypothetical_protein_1283867..1284097_NEGATIVE 229 36 9 47 20 NC_009009:SSA_1270|5end_Flavodoxin_1293916..1294146_NEGATIVE 229 46 9 225 184 NC_009009:SSA_1267|5end_crcB-like_protein_2,_putative_1291347..1291577_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 29 9 82 62 NC_009009:SSA_1111|3end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1137940..1138090_POSITIVE 267 130 81 57 13 NC_009009:SSA_0809|3end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791606..791756_POSITIVE 266 47 11 137 107 NC_009009:SSA_1936|3end_3-oxoacyl-[acyl-carrier_protein]_reductase,_putative_1923104..1923254_NEGATIVE 257 88 44 100 51 NC_009009:SSA_1578|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1582929..1583079_POSITIVE 254 98 53 45 4 NC_009009:SSA_2285|3end_hypothetical_protein_2287825..2287975_POSITIVE 252 178 138 51 13 NC_009009:SSA_1760|3end_hypothetical_protein_1747126..1747276_NEGATIVE 252 47 9 100 57 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 248 73 32 90 53 NC_009009:SSA_0732|3end_Transposase,_putative_715711..715861_NEGATIVE 244 46 3 108 63 NC_009009:SSA_0091|3end_V-type_sodium_ATPase,_subunit_A,_putative_92988..93138_POSITIVE 231 59 12 87 39 NC_009009:SSA_2190|3end_33_kDa_chaperonin,_putative_2192118..2192268_POSITIVE 231 70 33 148 112 NC_009009:SSA_1997|3end_Membrane_spanning_protein,_putative_1994162..1994312_NEGATIVE 231 90 49 85 51 NC_009009:SSA_1258|3end_Purine_nucleoside_phosphorylase,_family_1,_putative_1283858..1284008_NEGATIVE 227 100 51 48 2 NC_009009:SSA_0388|3end_Mismatch_repair_ATPase_(MutS_family),_putative_384248..384398_POSITIVE 226 91 56 68 35 NC_009009:SSA_0062|3end_Aldose_1-epimerase,_putative_64858..65008_POSITIVE 225 59 16 142 101 NC_009009:SSA_1581|3end_Metal-binding_ABC_transporter_(probably_hemin),_putative_1584770..1584920_POSITIVE 223 96 53 86 48 NC_009009:SSA_0871|3end_Cell_division_protein_FtsX,_putative_864627..864777_POSITIVE 222 100 51 74 9 NC_009009:SSA_0183|3end_hypothetical_protein_188106..188256_POSITIVE 221 83 44 36 2 NC_009009:SSA_2351|3end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_ATPase_component,_putative_2352785..2352935_NEGATIVE 219 28 1 113 92 NC_009009:SSA_0400|3end_hypothetical_protein_396470..396620_NEGATIVE 215 87 48 75 41 NC_009009:SSA_2209|3end_Penicillin-binding_protein_2A,_putative_2208144..2208294_NEGATIVE