Origin IGS: tgaaaaacccctttgtcacttacagcagctgacaaaggggttttttagtttattaatgcaagcaaaagacttttaccagtaaaatggtaaaagtcttgagtggaaagat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atctttccactcaagacttttaccattttactggtaaaagtcttttgcttgcattaataaactaaaaaacccctttgtcagctgctgtaagtgacaaaggggtttttca Mask Tandem Repeat Region ================================================ tgaaaaacccctttgtcacttacagcagctgacaaaggggttttttagtttattaatgcaagcaaaagacttttaccagtaaaatggtaaaagtcttgagtggaaagat Find is-nt database================================================ Query_seq: SSA_1582:SSA_1583|SSA_1582:SSA_1583:Esterase, alpha/beta hydrolase superfamily, putative:6-O-methylguanine-DNA methyltransferase, putative:-><-:1585504..1585612 109 tgaaaaacccctttgtcacttacagcagctgacaaaggggttttttagtttattaatgcaagcaaaagacttttaccagtaaaatggtaaaagtcttgagtggaaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1582:SSA_1583|SSA_1582:SSA_1583:Esterase, alpha/beta hydrolase superfamily, putative:6-O-methylguanine-DNA methyltransferase, putative:-><-:1585504..1585612 109 tgaaaaacccctttgtcacttacagcagctgacaaaggggttttttagtttattaatgcaagcaaaagacttttaccagtaaaatggtaaaagtcttgagtggaaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1582:SSA_1583|SSA_1582:SSA_1583:Esterase, alpha/beta hydrolase superfamily, putative:6-O-methylguanine-DNA methyltransferase, putative:-><-:1585504..1585612 109 tgaaaaacccctttgtcacttacagcagctgacaaaggggttttttagtttattaatgcaagcaaaagacttttaccagtaaaatggtaaaagtcttgagtggaaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaaaacccctttgtcacttacagcagctgacaaaggggttttttagtttattaatgcaagcaaaagacttttaccagtaaaatggtaaaagtcttgagtggaaagat Predict ORF larger than 30AA ================================================ tgaaaaacccctttgtcacttacagcagctgacaaaggggttttttagtttattaatgcaagcaaaagacttttaccagtaaaatggtaaaagtcttgagtggaaagat 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================================================ tgaaaaacccctttgtcacttacagcagctgacaaaggggttttttagtttattaatgcaagcaaaagacttttaccagtaaaatggtaaaagtcttgagtggaaagat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 68 HP_score: -8.3 Tail_Score: -3.08679 Start: 70 End: 93 Full_Region: AATGCAAGCAAAAGA CTTTTACCA GTAAAA TGGTAAAAG TCTTGAGTGGAAAGA .....................................................................CTTTTACCAGTAAAATGGTAAAAG................ Find igs database================================================ Query_seq: SSA_1582:SSA_1583|SSA_1582:SSA_1583:Esterase, alpha/beta hydrolase superfamily, putative:6-O-methylguanine-DNA methyltransferase, putative:-><-:1585504..1585612 109 tgaaaaacccctttgtcacttacagcagctgacaaaggggttttttagtttattaatgcaagcaaaagacttttaccagtaaaatggtaaaagtcttgagtggaaagat Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_009009_SSA_1582_SSA_1583|Esterase, alpha/beta hydrolase superfamily, putative:6-O-methylguanine-DNA methyltransferase, putative|POSITIVE:NEGATIVE|[1585504,1585612]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 tgaaaaacccctttgtcacttacagcagctgacaaaggggttttttagtttattaatgcaagcaaaagacttttaccagtaaaatggtaaaagtcttgagtggaaagat tgaaaaacccctttgtcacttacagcagctgacaaaggggttttttagtttattaatgcaagcaaaagacttttaccagtaaaatggtaaaagtcttgagtggaaagat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAAACCCCUUUGUCACUUACAGCAGCUGACAAAGGGGUUUUUUAGUUUAUUAAUGCAAGCAAAAGACUUUUACCAGUAAAAUGGUAAAAGUCUUGAGUGGAAAGAU ((((((((((((((((((((......)).))))))))))))))))))..............((..(((((((((((((......)))))))))))))..))........ (-45.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUUCCACUCAAGACUUUUACCAUUUUACUGGUAAAAGUCUUUUGCUUGCAUUAAUAAACUAAAAAACCCCUUUGUCAGCUGCUGUAAGUGACAAAGGGGUUUUUCA ............(((((((((((((......)))))))))))))....................((((((((((((((((.((......)))))))))))))))))).. (-40.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 50 11 230 183 NC_009009:SSA_2090|5end_Hexulose-6-phosphate_synthase,_putative_2095038..2095268_NEGATIVE 261 46 7 194 155 NC_009009:SSA_2301|5end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2303268..2303498_NEGATIVE 261 64 21 90 32 NC_009009:SSA_0715|5end_DNA_uptake_protein,_putative_700726..700956_POSITIVE 254 40 8 150 121 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 253 59 11 230 180 NC_009009:SSA_1445|5end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447886..1448116_NEGATIVE 251 46 11 88 56 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 250 50 1 63 7 NC_009009:SSA_0780|5end_Acid_phosphatase_(PAP2_family),_putative_764748..764978_POSITIVE 248 30 5 207 187 NC_009009:SSA_1489|5end_hypothetical_protein_1495788..1496018_NEGATIVE 245 44 9 39 5 NC_009009:SSA_1440|5end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444721..1444951_NEGATIVE 243 50 8 145 104 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 243 99 52 66 17 NC_009009:SSA_0187|5end_Competence_protein_ComYD,_putative_190350..190580_POSITIVE 242 49 9 138 103 NC_009009:SSA_1030|5end_Transcriptional_regulator,_TetR_family,_putative_1047094..1047324_POSITIVE 239 79 36 51 5 NC_009009:SSA_2056|5end_Cinnamoyl_ester_hydrolase,_putative_2058587..2058817_POSITIVE 236 48 5 131 95 NC_009009:SSA_0202|5end_hypothetical_protein_200534..200764_POSITIVE 231 50 6 75 25 NC_009009:SSA_1655|5end_hypothetical_protein_1651816..1652046_NEGATIVE 231 48 8 154 97 NC_009009:SSA_0125|5end_50S_ribosomal_protein_L30,_putative_116930..117160_POSITIVE 228 99 61 206 170 NC_009009:SSA_0437|5end_30S_ribosomal_protein_S6,_putative_440313..440543_POSITIVE 228 46 9 171 126 NC_009009:SSA_0353|5end_Conserved_uncharacterized_protein_345940..346170_POSITIVE 226 64 23 159 115 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 225 77 39 67 29 NC_009009:SSA_1572|5end_hypothetical_protein_1575908..1576138_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 485 47 1 90 44 NC_009009:SSA_1582|3end_Esterase,_alpha/beta_hydrolase_superfamily,_putative_1585443..1585593_POSITIVE 245 58 11 136 79 NC_009009:SSA_0170|3end_hypothetical_protein_168130..168280_NEGATIVE 243 99 52 94 45 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE 239 46 15 146 98 NC_009009:SSA_1808|3end_hypothetical_protein_1791394..1791544_NEGATIVE 238 59 11 146 94 NC_009009:SSA_2061|3end_Peptide_deformylase,_putative_2063259..2063409_POSITIVE 238 31 8 144 120 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 236 41 5 129 97 NC_009009:SSA_0343|3end_DNA-damage-inducible_protein_P,_putative_338669..338819_POSITIVE 236 48 5 129 93 NC_009009:SSA_0201|3end_ABC_multidrug_transporter_(3-component_subtilin_immunity_exporter),_putative_200612..200762_POSITIVE 231 69 23 60 8 NC_009009:SSA_1853|3end_S-ribosylhomocysteine_lyase,_putative_1849360..1849510_POSITIVE 231 48 8 140 83 NC_009009:SSA_0124|3end_30S_ribosomal_protein_S5,_putative_116996..117146_POSITIVE 225 50 4 89 49 NC_009009:SSA_0385|3end_ABC_transporter,_glycine-betaine/proline_permease_protein,_putative_378526..378676_NEGATIVE 223 39 7 144 110 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 222 48 1 123 74 NC_009009:SSA_0412|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_407255..407405_NEGATIVE 221 48 8 140 79 NC_009009:SSA_0107|3end_50S_ribosomal_protein_L3,_putative_108871..109021_POSITIVE 220 70 24 101 54 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 220 70 23 146 103 NC_009009:SSA_0639|3end_hypothetical_protein_627733..627883_NEGATIVE 220 50 8 119 75 NC_009009:SSA_0002|3end_DNA_polymerase_III,_beta_chain,_putative_2801..2951_POSITIVE 218 59 11 147 95 NC_009009:SSA_0212|3end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_209079..209229_POSITIVE 216 46 1 83 32 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 216 69 23 90 43 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE