Origin IGS: tggactggtgagggaacgcctataaatcaaaaaagactgaagaatctcagtcttttttgctggttcgagtattgcttgacttatgtttagtcaagaggtaaggttatttatcttgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcaagataaataaccttacctcttgactaaacataagtcaagcaatactcgaaccagcaaaaaagactgagattcttcagtcttttttgatttataggcgttccctcaccagtcca Mask Tandem Repeat Region ================================================ tggactggtgagggaacgcctataaatcaaaaaagactgaagaatctcagtcttttttgctggttcgagtattgcttgacttatgtttagtcaagaggtaaggttatttatcttgc Find is-nt database================================================ Query_seq: SSA_0325:SSA_0326|SSA_0325:SSA_0326:Membrane-anchored glycerophosphoryl diester phosphodiesterase, putative:Conserved uncharacterized BCR, YbaB family:-><-:319498..319613 116 tggactggtgagggaacgcctataaatcaaaaaagactgaagaatctcagtcttttttgctggttcgagtattgcttgacttatgtttagtcaagaggtaaggttatttatcttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0325:SSA_0326|SSA_0325:SSA_0326:Membrane-anchored glycerophosphoryl diester phosphodiesterase, putative:Conserved uncharacterized BCR, YbaB family:-><-:319498..319613 116 tggactggtgagggaacgcctataaatcaaaaaagactgaagaatctcagtcttttttgctggttcgagtattgcttgacttatgtttagtcaagaggtaaggttatttatcttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0325:SSA_0326|SSA_0325:SSA_0326:Membrane-anchored glycerophosphoryl diester phosphodiesterase, putative:Conserved uncharacterized BCR, YbaB family:-><-:319498..319613 116 tggactggtgagggaacgcctataaatcaaaaaagactgaagaatctcagtcttttttgctggttcgagtattgcttgacttatgtttagtcaagaggtaaggttatttatcttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggactggtgagggaacgcctataaatcaaaaaagactgaagaatctcagtcttttttgctggttcgagtattgcttgacttatgtttagtcaagaggtaaggttatttatcttgc Predict ORF larger than 30AA ================================================ tggactggtgagggaacgcctataaatcaaaaaagactgaagaatctcagtcttttttgctggttcgagtattgcttgacttatgtttagtcaagaggtaaggttatttatcttgc 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================================================ PromScan Matrix: RpoN Strand: + Score: 82 Start: 60 End: 76 ...........................................................CTGGTTCGAGTATTGCT........................................ tggactggtgagggaacgcctataaatcaaaaaagactgaagaatctcagtcttttttgctggttcgagtattgcttgacttatgtttagtcaagaggtaaggttatttatcttgc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -9.8 Tail_Score: -2.75535 Start: 27 End: 60 Full_Region: GGGAACGCCTATAAA TCAAAAAAGACTGA AGAATC TCAGTCTTTTTTGC TGGTTCGAGTATTGC ..........................TCAAAAAAGACTGAAGAATCTCAGTCTTTTTTGC........................................................ TransTerm Strand: - Conf: 85 HP_score: -6.3 Tail_Score: -5.42514 Start: 35 End: 52 Full_Region: cgaaccagcaaaaaa gactgag attc ttcagtc ttttttgatttatag ..................................gactgagattcttcagtc................................................................ Find igs database================================================ Query_seq: SSA_0325:SSA_0326|SSA_0325:SSA_0326:Membrane-anchored glycerophosphoryl diester phosphodiesterase, putative:Conserved uncharacterized BCR, YbaB family:-><-:319498..319613 116 tggactggtgagggaacgcctataaatcaaaaaagactgaagaatctcagtcttttttgctggttcgagtattgcttgacttatgtttagtcaagaggtaaggttatttatcttgc Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: NC_009009_SSA_0325_SSA_0326|Membrane-anchored glycerophosphoryl diester phosphodiesterase, putative:Conserved uncharacterized BCR, YbaB family|POSITIVE:NEGATIVE|[319498,319613]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 tggactggtgagggaacgcctataaatcaaaaaagactgaagaatctcagtcttttttgctggttcgagtattgcttgacttatgtttagtcaagaggtaaggttatttatcttgc tggactggtgagggaacgcctataaatcaaaaaagactgaagaatctcagtcttttttgctggttcgagtattgcttgacttatgtttagtcaagaggtaaggttatttatcttgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGACUGGUGAGGGAACGCCUAUAAAUCAAAAAAGACUGAAGAAUCUCAGUCUUUUUUGCUGGUUCGAGUAUUGCUUGACUUAUGUUUAGUCAAGAGGUAAGGUUAUUUAUCUUGC .((((..(..(((.....)))......(((((((((((((......))))))))))))))..))))........(((((((.......)))))))..(((((((.....))))))) (-36.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAGAUAAAUAACCUUACCUCUUGACUAAACAUAAGUCAAGCAAUACUCGAACCAGCAAAAAAGACUGAGAUUCUUCAGUCUUUUUUGAUUUAUAGGCGUUCCCUCACCAGUCCA ((...((((((..........(((((((.......)))))))...............((((((((((((((....))))))))))))))))))))..))................. (-27.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 99 51 193 137 NC_009009:SSA_1214|5end_Conserved_uncharacterized_Lactobacillales_protein_1237482..1237712_POSITIVE 276 75 33 54 13 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 274 89 49 132 93 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 272 77 33 189 129 NC_009009:SSA_1415|5end_Oxidoreductase,_putative_1426508..1426738_NEGATIVE 272 97 51 194 140 NC_009009:SSA_0939|5end_Inositol_monophosphatase_(Mg++_dependent),_putative_946810..947040_POSITIVE 271 79 44 127 95 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 261 100 52 83 39 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 260 98 53 96 41 NC_009009:SSA_1397|5end_hypothetical_protein_1410589..1410819_POSITIVE 251 87 41 170 117 NC_009009:SSA_0187|5end_Competence_protein_ComYD,_putative_190350..190580_POSITIVE 245 78 37 71 32 NC_009009:SSA_1087|5end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1104524..1104754_POSITIVE 245 100 57 214 161 NC_009009:SSA_1077|5end_N-acetyl-glucosamine_matabolism,_putative_1094979..1095209_POSITIVE 244 59 26 95 61 NC_009009:SSA_1600|5end_hypothetical_protein_1606595..1606825_NEGATIVE 244 76 34 70 4 NC_009009:SSA_0317|5end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311259..311489_POSITIVE 243 75 34 65 26 NC_009009:SSA_1062|5end_50S_ribosomal_protein_L27,_putative_1078284..1078514_POSITIVE 243 80 34 167 105 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 242 76 32 60 11 NC_009009:SSA_2260|5end_DNA_mismatch_repair_protein_hexA,_putative_2258150..2258380_NEGATIVE 242 102 67 44 11 NC_009009:SSA_1126|5end_Thiamine_biosynthesis_lipoprotein,_putative_1151522..1151752_NEGATIVE 239 91 56 85 52 NC_009009:SSA_1529|5end_Lysyl-tRNA_synthetase,_putative_1535871..1536101_POSITIVE 239 50 2 194 147 NC_009009:SSA_0744|5end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_726804..727034_NEGATIVE 238 75 33 54 8 NC_009009:SSA_2045|5end_Reductase,_putative_2048948..2049178_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 79 31 113 50 NC_009009:SSA_1630|3end_hypothetical_protein_1631508..1631658_POSITIVE 295 59 28 63 32 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 287 78 31 113 49 NC_009009:SSA_0592|3end_hypothetical_protein_584248..584398_POSITIVE 278 78 34 149 97 NC_009009:SSA_1626|3end_DNA_translocase_ftsK,_putative_1627077..1627227_NEGATIVE 276 75 33 51 10 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 274 89 49 122 83 NC_009009:SSA_0980|3end_3-isopropylmalate_dehydratase_large_subunit,_putative_985466..985616_POSITIVE 271 59 19 84 45 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 271 79 44 110 78 NC_009009:SSA_0278|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_272382..272532_POSITIVE 270 99 51 61 4 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 256 79 35 101 50 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 245 58 11 76 23 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 245 78 37 74 35 NC_009009:SSA_1086|3end_TRNA_nucleotidyltransferase,_putative_1104607..1104757_POSITIVE 244 59 26 98 64 NC_009009:SSA_1601|3end_VacB-like_protein,_putative_1606592..1606742_NEGATIVE 244 76 34 73 7 NC_009009:SSA_0316|3end_hypothetical_protein_311342..311492_POSITIVE 239 97 55 60 13 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 238 98 54 144 81 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 237 77 32 143 93 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 235 99 55 54 1 NC_009009:SSA_0430|3end_Cationic_amino_acid_transporter,_putative_431248..431398_NEGATIVE 232 78 35 56 9 NC_009009:SSA_0660|3end_Cell_division_protein_DivIVA,_putative_644672..644822_POSITIVE 230 38 3 67 29 NC_009009:SSA_1639|3end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1641339..1641489_NEGATIVE