Origin IGS: tgcaaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaaatgcgatagacattgtcatcatttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaatgatgacaatgtctatcgcattttaagtacactatccagcaagtctttccactataaaaggcatccagtcaaggttttcacacctgattggatgccttttttctgatgactagattttttgca Mask Tandem Repeat Region ================================================ tgcaaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaaatgcgatagacattgtcatcatttta Find is-nt database================================================ Query_seq: SMT_1466:SMT_1467|SMT_1466:SMT_1467:endopeptidase O:hydroxyacylglutathione hydrolase:-><-:1447966..1448093 128 tgcaaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaaatgcgatagacattgtcatcatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1466:SMT_1467|SMT_1466:SMT_1467:endopeptidase O:hydroxyacylglutathione hydrolase:-><-:1447966..1448093 128 tgcaaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaaatgcgatagacattgtcatcatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1466:SMT_1467|SMT_1466:SMT_1467:endopeptidase O:hydroxyacylglutathione hydrolase:-><-:1447966..1448093 128 tgcaaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaaatgcgatagacattgtcatcatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcaaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaaatgcgatagacattgtcatcatttta Predict ORF larger than 30AA ================================================ tgcaaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaaatgcgatagacattgtcatcatttta 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================================================ tgcaaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaaatgcgatagacattgtcatcatttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.5 Tail_Score: -5.31877 Start: 28 End: 64 Full_Region: ctttccactataaaa ggcatccagtcaaggt tttcac acctgattggatgcc ttttttctgatgact ...........................ggcatccagtcaaggttttcacacctgattggatgcc................................................................ Find igs database================================================ Query_seq: SMT_1466:SMT_1467|SMT_1466:SMT_1467:endopeptidase O:hydroxyacylglutathione hydrolase:-><-:1447966..1448093 128 tgcaaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaaatgcgatagacattgtcatcatttta Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: smit_SMT_1466_SMT_1467|endopeptidase O:hydroxyacylglutathione hydrolase|POSITIVE:NEGATIVE|[1447966,1448093]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 tgcaaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaaatgcgatagacattgtcatcatttta tgcaaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaaatgcgatagacattgtcatcatttta Inter-species Hit: Count: 3 Min: 1 Max: 102 Len: 102 Subject: NC_008533_SPD_1459_SPD_1460|metallo-beta-lactamase superfamily protein:endopeptidase O|POSITIVE:NEGATIVE|[1474313,1474434]|122 HSP 1 e-value: 2.0E-33 bit: 143.0 Len: 100 Query Start:3 Query End:102 Subject Strand: NEGATIVE Subject Start: 21 Subject End: 120 ..caaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaa.......................... ..caaaaaatctagtcatcagaaaaaaggcatccaatcacgtgtgaaaaccttgataggatgccttttataatagaaagatttgctggatagtttacttaaa.......................... Subject: NC_003098_spr1490_spr1491|hypothetical protein:Endopeptidase O|POSITIVE:NEGATIVE|[1466782,1466903]|122 HSP 1 e-value: 2.0E-33 bit: 143.0 Len: 100 Query Start:3 Query End:102 Subject Strand: NEGATIVE Subject Start: 21 Subject End: 120 ..caaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaa.......................... ..caaaaaatctagtcatcagaaaaaaggcatccaatcacgtgtgaaaaccttgataggatgccttttataatagaaagatttgctggatagtttacttaaa.......................... Subject: NC_003028_SP_1646_SP_1647|metallo-beta-lactamase superfamily protein:endopeptidase O|POSITIVE:NEGATIVE|[1545562,1545683]|122 HSP 1 e-value: 2.0E-32 bit: 139.0 Len: 102 Query Start:1 Query End:102 Subject Strand: NEGATIVE Subject Start: 21 Subject End: 122 tgcaaaaaatctagtcatcagaaaaaaggcatccaatcaggtgtgaaaaccttgactggatgccttttatagtggaaagacttgctggatagtgtacttaaa.......................... tgcaaaaaatctagtcatcagaaaaaaggcatccaatcatgtgtgaaaaccttgataggatgccttttgtaatagaaagatttgctggatagtttacttaaa.......................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAAAAAAUCUAGUCAUCAGAAAAAAGGCAUCCAAUCAGGUGUGAAAACCUUGACUGGAUGCCUUUUAUAGUGGAAAGACUUGCUGGAUAGUGUACUUAAA ((((....(((((((........((((((((((((.(((((.((....))))))).))))))))))))..(((......))).)))))))..))))...... (-35.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAGUACACUAUCCAGCAAGUCUUUCCACUAUAAAAGGCAUCCAGUCAAGGUUUUCACACCUGAUUGGAUGCCUUUUUUCUGAUGACUAGAUUUUUUGCA .................((((((((...(((...((((((((((((((((.(((......)))))))))))))))))))....).))...))))...)))). (-34.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 95 51 72 25 smit:SMT_145|5end_hypothetical_protein_95873..96103_POSITIVE 281 88 41 221 169 smit:SMT_1351|5end_dephospho-CoA_kinase_1329817..1330047_NEGATIVE 277 69 29 53 12 smit:SMT_804|5end_S-adenosylmethionine_synthetase_715074..715304_NEGATIVE 264 90 41 69 4 smit:SMT_1176|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1128993..1129223_NEGATIVE 260 98 56 166 121 smit:SMT_1642|5end_K03497_chromosome_partitioning_protein,_ParB_family_1628996..1629226_NEGATIVE 254 56 19 62 19 smit:SMT_1625|5end_DNA_polymerase_IV_1613925..1614155_POSITIVE 253 79 31 71 18 smit:SMT_523|5end_K02004_447422..447652_POSITIVE 252 70 28 201 136 smit:SMT_1291|5end_hypothetical_protein_1253875..1254105_POSITIVE 251 80 34 174 136 smit:SMT_704|5end_Cof_family_protein_613662..613892_POSITIVE 251 43 3 146 105 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 251 43 3 146 105 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 246 59 11 70 24 smit:SMT_775|5end_alpha-acetolactate_decarboxylase_685972..686202_NEGATIVE 244 95 52 53 6 smit:SMT_596|5end_K03976_putative_transcription_regulator_513075..513305_NEGATIVE 241 76 33 59 21 smit:SMT_1376|5end_tetrapyrrole_(corrin/porphyrin)_methylase_family_protein_1355553..1355783_NEGATIVE 241 99 61 139 96 smit:SMT_289|5end_glycosyltransferase_232184..232414_POSITIVE 237 92 51 54 22 smit:SMT_506|5end_K07729_putative_transcriptional_regulator_437635..437865_NEGATIVE 237 92 51 54 22 smit:SMT_503|5end_K07729_putative_transcriptional_regulator_436204..436434_NEGATIVE 234 98 51 71 5 smit:SMT_1446|5end_pneumococcal_vaccine_antigen_A_1429610..1429840_NEGATIVE 234 64 28 72 30 smit:SMT_1274|5end_K02008_cobalt_transport_system_permease_protein_1237741..1237971_POSITIVE 234 100 51 224 174 smit:SMT_508|5end_hypothetical_protein_438620..438850_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 466 68 21 67 20 smit:SMT_1977|3end_endopeptidase_O_1908454..1908604_POSITIVE 422 68 24 67 23 smit:SMT_1466|3end_endopeptidase_O_1447905..1448055_POSITIVE 295 70 23 58 10 smit:SMT_1615|3end_K02016_iron_complex_transport_system_substrate-binding_protein_1601734..1601884_NEGATIVE 263 80 36 77 33 smit:SMT_937|3end_dipeptidase_890741..890891_POSITIVE 263 46 2 62 24 smit:SMT_781|3end_hypothetical_protein_689509..689659_NEGATIVE 262 58 17 67 28 smit:SMT_735|3end_putative_transposase,_ISSmu1_641395..641545_POSITIVE 253 79 31 69 16 smit:SMT_522|3end_K02003_447500..447650_POSITIVE 250 68 21 71 22 smit:SMT_779|3end_ribonuclease_BN,_putative_687883..688033_NEGATIVE 244 95 52 53 6 smit:SMT_597|3end_K08974_putative_membrane_protein_513075..513225_NEGATIVE 241 76 33 56 18 smit:SMT_1377|3end_hypothetical_protein_1355556..1355706_NEGATIVE 241 99 61 128 85 smit:SMT_288|3end_hypothetical_protein_232253..232403_POSITIVE 237 92 51 51 19 smit:SMT_507|3end_hypothetical_protein_437638..437788_NEGATIVE 237 92 51 51 19 smit:SMT_504|3end_hypothetical_protein_436207..436357_NEGATIVE 236 68 23 88 45 smit:SMT_1814|3end_amino_acid_transporter_1788640..1788790_POSITIVE 234 98 51 71 5 smit:SMT_1447|3end_hypothetical_protein_1429610..1429760_NEGATIVE 234 64 28 79 37 smit:SMT_1273|3end_K02006_cobalt_transport_system_ATP-binding_protein_1237828..1237978_POSITIVE 232 75 32 150 98 smit:SMT_685|3end_LPS_biosynthesis_protein_595237..595387_POSITIVE 231 65 26 101 65 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 230 90 42 88 43 smit:SMT_817|3end_aminotransferase_727533..727683_NEGATIVE 229 50 12 85 49 smit:SMT_564|3end_23S_rRNA_Gm2251_methyltransferase_481989..482139_NEGATIVE