Origin IGS: aatgattataatccccttccaattgaaaaaaattaagactgatctgaattcgcattacccactcaacgacttttagccaacatgaattaccaagtgttttggcctgaaaagtcagaaatttgagactagtttgcttgcttaatcccaaatcgttctaaccaactgcgtttaaacaaattcttcttgctttagttgggaagaactttgttttttttttagaaatatctaagccaatcttcttttgacatagatattctcctatccttaatttattatactactatagtatacaaaaaaagggccggaaattcaatctattccggcatctgctcttcttaatcgcttg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 caagcgattaagaagagcagatgccggaatagattgaatttccggccctttttttgtatactatagtagtataataaattaaggataggagaatatctatgtcaaaagaagattggcttagatatttctaaaaaaaaaacaaagttcttcccaactaaagcaagaagaatttgtttaaacgcagttggttagaacgatttgggattaagcaagcaaactagtctcaaatttctgacttttcaggccaaaacacttggtaattcatgttggctaaaagtcgttgagtgggtaatgcgaattcagatcagtcttaatttttttcaattggaaggggattataatcatt Mask Tandem Repeat Region ================================================ aatgattataatccccttccaattgaaaaaaattaagactgatctgaattcgcattacccactcaacgacttttagccaacatgaattaccaagtgttttggcctgaaaagtcagaaatttgagactagtttgcttgcttaatcccaaatcgttctaaccaactgcgtttaaacaaattcttcttgctttagttgggaagaactttgttttttttttagaaatatctaagccaatcttcttttgacatagatattctcctatccttaatttattatactactatagtatacaaaaaaagggccggaaattcaatctattccggcatctgctcttcttaatcgcttg Find is-nt database================================================ Query_seq: SSA_1277:SSA_1278|SSA_1277:SSA_1278:D-alanyl-D-alanine carboxypeptidase:Rhodanese-like domain protein, putative:<-<-:1299307..1299652 346 aatgattataatccccttccaattgaaaaaaattaagactgatctgaattcgcattacccactcaacgacttttagccaacatgaattaccaagtgttttggcctgaaaagtcagaaatttgagactagtttgcttgcttaatcccaaatcgttctaaccaactgcgtttaaacaaattcttcttgctttagttgggaagaactttgttttttttttagaaatatctaagccaatcttcttttgacatagatattctcctatccttaatttattatactactatagtatacaaaaaaagggccggaaattcaatctattccggcatctgctcttcttaatcgcttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1277:SSA_1278|SSA_1277:SSA_1278:D-alanyl-D-alanine carboxypeptidase:Rhodanese-like domain protein, putative:<-<-:1299307..1299652 346 aatgattataatccccttccaattgaaaaaaattaagactgatctgaattcgcattacccactcaacgacttttagccaacatgaattaccaagtgttttggcctgaaaagtcagaaatttgagactagtttgcttgcttaatcccaaatcgttctaaccaactgcgtttaaacaaattcttcttgctttagttgggaagaactttgttttttttttagaaatatctaagccaatcttcttttgacatagatattctcctatccttaatttattatactactatagtatacaaaaaaagggccggaaattcaatctattccggcatctgctcttcttaatcgcttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1277:SSA_1278|SSA_1277:SSA_1278:D-alanyl-D-alanine carboxypeptidase:Rhodanese-like domain protein, putative:<-<-:1299307..1299652 346 aatgattataatccccttccaattgaaaaaaattaagactgatctgaattcgcattacccactcaacgacttttagccaacatgaattaccaagtgttttggcctgaaaagtcagaaatttgagactagtttgcttgcttaatcccaaatcgttctaaccaactgcgtttaaacaaattcttcttgctttagttgggaagaactttgttttttttttagaaatatctaagccaatcttcttttgacatagatattctcctatccttaatttattatactactatagtatacaaaaaaagggccggaaattcaatctattccggcatctgctcttcttaatcgcttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgattataatccccttccaattgaaaaaaattaagactgatctgaattcgcattacccactcaacgacttttagccaacatgaattaccaagtgttttggcctgaaaagtcagaaatttgagactagtttgcttgcttaatcccaaatcgttctaaccaactgcgtttaaacaaattcttcttgctttagttgggaagaactttgttttttttttagaaatatctaagccaatcttcttttgacatagatattctcctatccttaatttattatactactatagtatacaaaaaaagggccggaaattcaatctattccggcatctgctcttcttaatcgcttg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 247 End: 336 ...................................................................................................................................................................................................................................................... M D I L L S L I Y Y T T I V Y K K R A G N S I Y S G I C S S .......... Protein_Len: 35 Strand: - Start: 158 End: 262 ............................................................................................................................................................. G V A N L C I R R A K T P F F K T K K K S I D L G I K K Q C L Y E G M .................................................................................... Protein_Len: 49 Strand: - Start: 2 End: 148 . H N Y D G E L Q F F N L S I Q I R M V W E V V K L W C S N G L T K A Q F T L F K L S T Q K S L G M ...................................................................................................................................................................................................... aatgattataatccccttccaattgaaaaaaattaagactgatctgaattcgcattacccactcaacgacttttagccaacatgaattaccaagtgttttggcctgaaaagtcagaaatttgagactagtttgcttgcttaatcccaaatcgttctaaccaactgcgtttaaacaaattcttcttgctttagttgggaagaactttgttttttttttagaaatatctaagccaatcttcttttgacatagatattctcctatccttaatttattatactactatagtatacaaaaaaagggccggaaattcaatctattccggcatctgctcttcttaatcgcttg 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: 84 Start: 285 End: 314 ............................................................................................................................................................................................................................................................................................ATTGAATTTCCGGCCCTTTTTTTGTATACT................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatgattataatccccttccaattgaaaaaaattaagactgatctgaattcgcattacccactcaacgacttttagccaacatgaattaccaagtgttttggcctgaaaagtcagaaatttgagactagtttgcttgcttaatcccaaatcgttctaaccaactgcgtttaaacaaattcttcttgctttagttgggaagaactttgttttttttttagaaatatctaagccaatcttcttttgacatagatattctcctatccttaatttattatactactatagtatacaaaaaaagggccggaaattcaatctattccggcatctgctcttcttaatcgcttg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -3.4 Tail_Score: -2.8499 Start: 90 End: 102 Full_Region: ttctgacttttcagg ccaa aacac ttgg taattcatgttggct .........................................................................................ccaaaacacttgg.................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 54 HP_score: -3.4 Tail_Score: -3.85698 Start: 223 End: 253 Full_Region: ttaaggataggagaa tatctatgtcaa aagaaga ttggcttagata tttctaaaaaaaaaa ..............................................................................................................................................................................................................................tatctatgtcaaaagaagattggcttagata............................................................................................. Find igs database================================================ Query_seq: SSA_1277:SSA_1278|SSA_1277:SSA_1278:D-alanyl-D-alanine carboxypeptidase:Rhodanese-like domain protein, putative:<-<-:1299307..1299652 346 aatgattataatccccttccaattgaaaaaaattaagactgatctgaattcgcattacccactcaacgacttttagccaacatgaattaccaagtgttttggcctgaaaagtcagaaatttgagactagtttgcttgcttaatcccaaatcgttctaaccaactgcgtttaaacaaattcttcttgctttagttgggaagaactttgttttttttttagaaatatctaagccaatcttcttttgacatagatattctcctatccttaatttattatactactatagtatacaaaaaaagggccggaaattcaatctattccggcatctgctcttcttaatcgcttg Intra-Species Hit: Count: 1 Min: 1 Max: 346 Len: 346 Subject: NC_009009_SSA_1277_SSA_1278|D-alanyl-D-alanine carboxypeptidase:Rhodanese-like domain protein, putative|NEGATIVE:NEGATIVE|[1299307,1299652]|346 HSP 1 e-value: 1.0E-153 bit: 543.0 Len: 346 Query Start:1 Query End:346 Subject Strand: POSITIVE Subject Start: 1 Subject End: 346 aatgattataatccccttccaattgnnnnnnnttaagactgatctgaattcgcattacccactcaacgacttttagccaacatgaattaccaagtgttttggcctgaaaagtcagaaatttgagactagtttgcttgcttaatcccaaatcgttctaaccaactgcgtttaaacaaattcttcttgctttagttgggaagaactttgnnnnnnnnnnagaaatatctaagccaatcttcttttgacatagatattctcctatccttaatttattatactactatagtatacnnnnnnngggccggaaattcaatctattccggcatctgctcttcttaatcgcttg aatgattataatccccttccaattgaaaaaaattaagactgatctgaattcgcattacccactcaacgacttttagccaacatgaattaccaagtgttttggcctgaaaagtcagaaatttgagactagtttgcttgcttaatcccaaatcgttctaaccaactgcgtttaaacaaattcttcttgctttagttgggaagaactttgttttttttttagaaatatctaagccaatcttcttttgacatagatattctcctatccttaatttattatactactatagtatacaaaaaaagggccggaaattcaatctattccggcatctgctcttcttaatcgcttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUUAUAAUCCCCUUCCAAUUGAAAAAAAUUAAGACUGAUCUGAAUUCGCAUUACCCACUCAACGACUUUUAGCCAACAUGAAUUACCAAGUGUUUUGGCCUGAAAAGUCAGAAAUUUGAGACUAGUUUGCUUGCUUAAUCCCAAAUCGUUCUAACCAACUGCGUUUAAACAAAUUCUUCUUGCUUUAGUUGGGAAGAACUUUGUUUUUUUUUUAGAAAUAUCUAAGCCAAUCUUCUUUUGACAUAGAUAUUCUCCUAUCCUUAAUUUAUUAUACUACUAUAGUAUACAAAAAAAGGGCCGGAAAUUCAAUCUAUUCCGGCAUCUGCUCUUCUUAAUCGCUUG ...(((((......((((...........((((((((.....((((((..((((.............(((((((.((((((((..........))))..))))...))))))).((((((((.((..(((......)))...)).)))))..)))........))))...(((((((((((((((((....).))))))))).)))))))....))))))((((((((.(.(((.......))).).))))))))........))))))))..(((((((...)))))))......))))(((((((..........)))))))............)))))..... (-68.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGCGAUUAAGAAGAGCAGAUGCCGGAAUAGAUUGAAUUUCCGGCCCUUUUUUUGUAUACUAUAGUAGUAUAAUAAAUUAAGGAUAGGAGAAUAUCUAUGUCAAAAGAAGAUUGGCUUAGAUAUUUCUAAAAAAAAAACAAAGUUCUUCCCAACUAAAGCAAGAAGAAUUUGUUUAAACGCAGUUGGUUAGAACGAUUUGGGAUUAAGCAAGCAAACUAGUCUCAAAUUUCUGACUUUUCAGGCCAAAACACUUGGUAAUUCAUGUUGGCUAAAAGUCGUUGAGUGGGUAAUGCGAAUUCAGAUCAGUCUUAAUUUUUUUCAAUUGGAAGGGGAUUAUAAUCAUU .....((((..(((((((....(((((((..........)))))))((((..(((((((((((...)))))).)))))..))))...(((((.((((((.(((((.......))))).)))))))))))..............)))))))................((((((((....((.((.(..(..(((..((((((((((((...........)))))))))))))))(((((((..((((((......(((....)))..))))))))))))).)..).)).))...)))))))).)))).....(((((((((((.....)))))))))))........ (-88.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 864 90 41 181 132 NC_009009:SSA_1277|5end_D-alanyl-D-alanine_carboxypeptidase_1299216..1299446_NEGATIVE 311 79 34 46 4 NC_009009:SSA_0958|5end_hypothetical_protein_967273..967503_POSITIVE 309 337 293 153 102 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 304 78 36 86 49 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 304 334 298 42 7 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 300 335 298 37 10 NC_009009:SSA_0566|5end_GTP-sensing_transcriptional_pleiotropic_repressor,_putative_560017..560247_POSITIVE 293 144 101 65 17 NC_009009:SSA_0546|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_540852..541082_POSITIVE 288 340 299 58 8 NC_009009:SSA_1165|5end_Transcriptional_regulator,_GntR_family,_putative_1191087..1191317_POSITIVE 279 334 291 63 13 NC_009009:SSA_1913|5end_Xanthine/uracil_permease_family_protein,_putative_1904666..1904896_NEGATIVE 278 328 290 208 174 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 278 330 298 67 33 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 275 167 125 58 15 NC_009009:SSA_1607|5end_Formamidopyrimidine-DNA_glycosylase,_putative_1613255..1613485_NEGATIVE 273 189 144 85 45 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 270 337 295 197 145 NC_009009:SSA_2044|5end_Cysteinyl-tRNA_synthetase,_putative_2048409..2048639_NEGATIVE 270 140 101 67 16 NC_009009:SSA_2038|5end_hypothetical_protein_2041627..2041857_POSITIVE 270 338 300 157 126 NC_009009:SSA_1372|5end_hypothetical_protein_1389137..1389367_NEGATIVE 270 249 204 112 62 NC_009009:SSA_0455|5end_Sucrose-6-phosphate_hydrolase,_putative_458450..458680_NEGATIVE 268 140 94 161 114 NC_009009:SSA_1804|5end_NADPH-flavin_oxidoreductase,_putative_1788668..1788898_NEGATIVE 268 167 121 56 10 NC_009009:SSA_0175|5end_Penicillin-binding_protein_1B,_putative_172152..172382_POSITIVE 266 332 299 231 192 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 334 298 55 20 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 298 200 151 88 31 NC_009009:SSA_1540|3end_hypothetical_protein_1544915..1545065_NEGATIVE 295 331 295 88 47 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 293 144 101 63 15 NC_009009:SSA_0544|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase,_putative_540930..541080_POSITIVE 278 328 290 72 38 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 278 330 298 51 17 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 264 335 300 40 8 NC_009009:SSA_1805|3end_Primosomal_protein_DnaI,_putative_1788665..1788815_NEGATIVE 261 164 121 148 95 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 259 265 223 140 99 NC_009009:SSA_1484|3end_DNA_ligase,_putative_1490230..1490380_NEGATIVE 258 240 191 73 29 NC_009009:SSA_1468|3end_3-dehydroquinate_synthase,_putative_1474385..1474535_NEGATIVE 258 165 122 115 76 NC_009009:SSA_0495|3end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_496036..496186_POSITIVE 256 185 145 149 120 NC_009009:SSA_1939|3end_Acyl_carrier_protein,_putative_1925875..1926025_NEGATIVE 256 339 295 131 76 NC_009009:SSA_1134|3end_Xanthine_phosphoribosyltransferase,_putative_1160316..1160466_POSITIVE 250 210 163 96 48 NC_009009:SSA_0177|3end_DNA-directed_RNA_polymerase_I,_beta_chain_(160_kDa_subunit),_putative_182132..182282_POSITIVE 249 340 291 95 33 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 249 334 294 74 41 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 248 134 93 44 1 NC_009009:SSA_2168|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+],_putative_2168563..2168713_POSITIVE 247 116 80 106 65 NC_009009:SSA_1913|3end_Xanthine/uracil_permease_family_protein,_putative_1903245..1903395_NEGATIVE 247 340 296 48 13 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 247 109 63 149 110 NC_009009:SSA_0116|3end_30S_ribosomal_protein_S17,_putative_112972..113122_POSITIVE